Computer tools and databases

2D molecular visualization (chemicals and macromolecules)

  • LeView: protein-ligand (standalone)
  • ChemPixCH: Hand Drawn Hydrocarbon Recognition (image to smiles) (standalone)
  • DECIMER Image Transformer V2: Deep Learning for Chemical Image Recognition (image to smiles) (standalone)
  • ChemSAM: Automated molecular structure segmentation from documents (image to smiles) (standalone)
  • YoDe-Segmentation: automated noise-free retrieval of molecular structures from scientific publications (standalone)
  • SwinOCSR: end-to-end optical chemical structure recognition using a Swin Transformer (standalone)
  • DECIMER—hand-drawn molecule: images dataset (dataset)
  • Img2Mol: accurate SMILES recognition from molecular graphical depictions (image to smiles) (standalone)
  • DECIMER: online image to SMILES (image to smiles) (online)
  • PIKAChU: a Python-based Informatics Kit for Analyzing Chemical Units (standalone)
  • Molecule Cloud Generator: cloud generator for small molecules in Smiles (online)
  • CIME: ChemInformatics Model Explorer, exploratory analysis of chemical model explanations (standalone)
  • IBS 2.0: an upgraded illustrator for the visualization of biological sequences (online)
  • Img2Mol: Accurate SMILES Recognition from Molecular Graphical Depictions (standalone)
  • VRNetzer: enables interactive network analysis in Virtual Reality (standalone)
  • multiSLIDE: multi-omics data visualization (standalone)
  • H2V: a database of human genes and proteins that respond to SARS‑CoV‑2, SARS‑CoV, and MERS‑CoV infection (Covid-19) (online)
  • CyTargetLinker: Extend biological networks (e.g., a disease network with Chembl or drugbank compounds) in Cytoscape (standalone)
  • Smi2DepictWeb: Smi2Depict tool of ChemDB Chemoinformatics Portal to see compound Smiles in 2D (online)
  • SMARTS-plus: A Toolbox for Chemical Pattern Design (online)
  • CONAN: A web application to detect specificity determinants and functional sites by amino acids co-variation network analysis (online)
  • Servier Medical Art: Free medical images provided by Servier (standalone)
  • bioRENDER: Professional medical art images (commercial) (online)
  • I-PV: a CIRCOS module for interactive protein sequence visualization (standalone, Circos installation can be relatively challenging on some OS!!)
  • TMAP: A new data visualization method, TMAP, capable of representing data sets of up to millions of data points and arbitrary high dimensionality as a two-dimensional tree. Visualizations based on TMAP are better suited than t-SNE or UMAP for the exploration and interpretation of large data sets due to their tree-like nature. The Python source code for TMAP is available on GitHub (https://github.com/reymond-group/tmap)
  • Circoletto: visualising sequence similarity with Circos - dataviz (online)
  • Circos Table Viewer: circular Visualization of Tabular Data (eg, sequences - dataviz) (online)
  • Galaxy Europe: Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research (online)
  • PoseView: protein-ligand data visualization (online)
  • NCIPLOT4: used to investigate noncovalent interactions (NCI) (i.e. hydrogen bonds, steric clashes and van der Waals) in systems ranging from small molecules to large biosystems (standalone)
  • Ketcher: Ketcher is a web-based chemical structure editor (standalone and for the web)
  • ReactomeFIViz: drug-target visualization in the context of pathways and networks (integrates drug-target interaction information with high quality manually curated pathways and a genome-wide human functional interaction network). Both the pathways and the functional interaction network are provided by Reactome (Reactome Cytoscape app standalone)
  • PyPathway: Python Package for Biological Network Analysis and Visualization (Reactome, WikiPathway, STRING, and BioGRID) (standalone)
  • CompNet: a GUI based tool for comparison of multiple biological interaction networks (standalone Windows or Linux, requires R and R igraph)
  • C-SPADE: web-application serves as an interactive and innovative visualization tool for drug screening data (online)
  • WebGraphviz: Graphviz is open source graph visualization software in a Browser (online)
  • PLEXVIEW: Make 2D diagrams of protein-ligand interactions (Hbonds, cation-pi) (online)
  • ezCADD: a Rapid 2D/3D Visualization Enabled Web Modeling Environment for Democratizing Computer-Aided Drug Design (small molecule docking, protein docking, 2D/3D interaction viz, de novo lead optimization, pocket search and polypharmacology) online
  • Chemicool: Periodic Table Key (online)
  • WebElements: Periodic Table Key (online)
  • ToxPi: ToxPi Graphical User Interface 2.0, Dynamic exploration, visualization, and sharing of integrated data models (standalone)
  • SmilesDrawer: parsing and drawing SMILES-encoded molecular structures using client-side JavaScript (standalone)
  • PathVisio: free open-source biological pathway analysis software that allows you to draw, edit and analyze biological pathways (standalone)
  • JME: JME Molecular Editor, draw and view chemicals (online)
  • PubChem Sketcher: A web-based tool for chemical sketching...(online)
  • Molinspiration: draw and view small molecules, predict 3D...(online)
  • Chemfig: draw molecules with easy syntax (standalone)
  • Chemtool: program for drawing chemical structures (standalone)
  • Molsketch: 2D molecular editing tool (standalone)
  • JChemPaint: chemical 2D structure editor (standalone)
  • SketchEl: interactive chemical molecule sketching tool (standalone)
  • BKchem: chemical drawing program (standalone)
  • DataWarrior: open-source data visualization and analysis program with embedded chemical intelligence (standalone)
  • NAViGaTOR: Network Analysis, Visualization and Graphing TORonto (standalone)
  • Cytoscape: open source software platform for visualizing complex networks and integrating these with any type of attribute data (standalone)
  • Diversity Genie: tool to analyze datasets of small organic molecules (collection diversity...) (standalone)
  • ChemAxon: software solutions and services for chemistry and biology (standalone)
  • ProViz: interactive exploration tool for investigating the functional and evolutionary features of proteins (online)
  • SkyAlign: tool for creating logos representing both sequence alignments and profile hidden Markov models (online)
  • RaacLogo: A New Sequence Logo Generator by Using Reduced Amino Acid Clusters (online)
  • cSeqLogo: Generation of consensus referenced two-sample Sequence Logos (online)
  • Topo2: transmembrane protein display (online)
  • TMRPres2D: TransMembrane protein Re-Presentation in 2 Dimensions (standalone)
  • Pro-origami: system for automatically generating protein structure cartoons in 2D (online)
  • CheS-Mapper: 3D-viewer for chemical datasets with small compounds (standalone)
  • FragVLib: Mining software for generating Fragment-based Virtual Library using pocket similarity search of ligand-receptor complexes (standalone)
  • ChemTreeMap : hierachical tree visualization of a molecule library (standalone)
  • Scaffold Hunter: software tool for the analysis of structure-related biochemical data (standalone)
  • ScaffoldGraph: an Open-Source Library (2020) for the Generation and Analysis of Molecular Scaffold Networks and Scaffold Trees (needs RDKIT) (standalone)
  • RJSplot: Interactive Graphs with R, data visualization(standalone)
  • OMNIDEPICT: 2D Chemical Depiction of Complex Molecules (SDG algorithm) (online)
  • ChemCom: compare compounds (standalone)
  • MONGKIE: integrated network analysis and visualization platform for multi-omics data (standalone)
  • CellDesigner: a structured diagram editor for drawing gene-regulatory and biochemical networks (standalone)
  • RING 2: residue interaction network (online)
  • RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles (online)
  • ANCA: a Web Server for Amino Acid Networks Construction and Analysis (online)
  • webPSN v2.0: a Webserver to Infer Fingerprints of Structural Communication in Biomacromolecules (proteins and nucleic acids, along the line of residue interaction networks but on dynamic system) (online)
  • ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism (online)
  • NAPS: Network Analysis of Protein Structures (online)
  • RINspector: a Cytoscape app for centrality analyses and DynaMine flexibility prediction with Chimera RINanalyser etc) (standalone)
  • RINerator and RINalyzer: analyzing and visualizing residue interaction networks in proteins (standalone)
  • Protein Contacts Atlas (PCA): tool to analyze and visualize protein structures at atomic resolution using residue-residue interaction networks (online)
  • eMolFrag: Decomposing Small Molecules for Fragment-Based Drug Design (standalone)
  • eMolFrag: Decomposing Small Molecules for Fragment-Based Drug Design (online)
  • Protein Lounge: pathways data visualization (commercial) (online)
  • Pathview Web: pathway visualization & data integration (online)
  • Minepath.org: interactive pathway analysis (online)
  • LigPlot+: view protein-ligand interactions in 2D (standalone)
  • Cell Signaling: pathways, data visualization (online)

Some sequence tools (mainly online 3D or 2D)

  • Scratch: almost Perfect Prediction of Protein Secondary Structure and Relative Solvent Accessibility Using Profiles, Deep Learning, and Structural Similarity (online)
  • pLM-BLAST: pLM-BLAST-distant homology detection based on direct comparison of sequence representations from protein language models (standalone)
  • PROST: improved global protein homolog detection with major gains in function identification (online)
  • DEPICTER2: a comprehensive webserver for intrinsic disorder and disorder function prediction (online)
  • COMER: protein analysis by homology (online)
  • NetSurfP: accurate and fast prediction of protein structural features by protein language models and deep learning (online)
  • OrthoQuantum: visualizing evolutionary repertoire of eukaryotic proteins (online)
  • MetaLogo: a heterogeneity-aware sequence logo generator and aligner (online)
  • MetaLogo: a heterogeneity-aware sequence logo generator and aligner (standalone)
  • Leri: A web-server for identifying protein functional networks from evolutionary couplings (dataviz) (online)
  • PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences (online)
  • COVID-19 Viral Genome Analysis Pipeline: tools for exploring accruing mutations in hCoV-19 (SARS-CoV-2) geographically and over time, with an emphasis on the Spike protein (sequences), using data from GISAID (online)
  • ProteoVision: web server for advanced visualization (topology, MSA, 3D…) of ribosomal proteins (or other proteins) (online)
  • DomainViz: intuitive visualization of consensus domain distributions across groups of proteins (online)
  • RaacLogo: a new sequence logo generator by using reduced amino acid clusters (online)
  • Martini 3: coarse-grained force field (standalone)
  • Multiple sequence alignment (MSA): alignment of three or more biological sequences (EMBL-EBI) (online)
  • MEDUSA: Multiclass flexibility prediction from sequences of amino acids (online)
  • FireProtASR: A Web Server for Fully Automated Ancestral Sequence Reconstruction (phylogeny-based analysis; protein stability) (online)
  • ENDscript 2: extracts and renders a comprehensive analysis of primary to quaternary protein structure information in an automated way (online)
  • AlgPred 2.0: an improved method for predicting allergenic proteins and mapping of IgE epitopes (online)
  • SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning (online)
  • DMFpred: Predicting protein disorder molecular functions based on protein cubic language model (online)
  • SolupHred: A Server to Predict the pH-dependent Aggregation of Intrinsically Disordered Proteins (online)
  • CONAN: A web application to detect specificity determinants and functional sites by amino acids co-variation network analysis (online)
  • DISOselect: Disorder Predictor Selection at the Protein Level (online)
  • TREND: a platform for exploring protein function in prokaryotes based on phylogenetic, domain architecture and gene neighborhood analyses (online)
  • IUPred2A: Prediction of Intrinsically Unstructured Proteins (and fonctional roles via Anchor2 such as PPI or protein-DNA interaction) (online)
  • IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation (online)
  • MusiteDeep: A Deep-Learning Based Webserver for Protein Post-Translational Modification Site Prediction and Visualization (online, input sequence) (standalone: https://github.com/duolinwang/MusiteDeep_web)
  • PL-search: Protein Remote Homology Detection (online)
  • PlaToLoCo: The First Web Meta-Server for Visualization and Annotation of Low Complexity Regions in Proteins (online)
  • Fuzzle: Identification and Analysis of Natural Building Blocks for Evolution-Guided Fragment-Based Protein Design (Fold Puzzle Database) (visualize protein universe…, protein fragment) (online)
  • Fuzzle2.0: Ligand Binding in Natural Protein Building Blocks (online)
  • Brewery: Deep Learning and Deeper Profiles for the Prediction of 1D Protein Structure Annotations (Prediction of protein structural features) (standalone and online)
  • POLYVIEW-2D: visualization tool for structural and functional annotations of proteins (online)
  • POLYVIEW-3D: visualization tool for structural and functional annotations of proteins (online)
  • Salign: A multiple protein sequence-structure alignment server (online)
  • Jalview: sequence analysis (standalone)
  • ESPript: Easy Sequencing in PostScript is a program which renders sequence similarities and secondary structure information from aligned sequences as a figure ready for publication (sequence to structure annotation) (online)
  • grabseqs: Simple downloading of reads and metadata from multiple next-generation sequencing data repositories (python) (standalone)
  • ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis (standalone)
  • ProFunc: Protein function prediction from protein 3D structure (online)
  • SAS: Sequence Annotated by Structure (online)
  • Scorecons: Calculation of residue conservation from multiple sequence alignment (online)
  • PROMALS3D: multiple sequence and structure alignment server (online)
  • TM-align: sequence independent protein structure comparisons (compare PDB structure) (online)
  • Alignment-Annotator: rendering and annotating sequence alignments (online)
  • Protein Residue Conservation Prediction: needs aligned sequence as input (Bioinformatics, 23(15):1875-82, 2007) (online still running?)
  • ProtrWeb: Compute Protein Sequence-Derived Structural and Physicochemical Descriptors (input sequence) (online)
  • Sibe: a computation tool to apply protein sequence statistics to predict folding and design in silico (online)
  • UniprotR: Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProt knowledgebase) (standalone)
  • SPIDER2: A Package to Predict Secondary Structure, Accessible Surface Area, and Main-Chain Torsional Angles by Deep Neural Networks (online and standalone)
  • BCrystal: An Interpretable Sequence-Based Protein Crystallization Predictor (standalone)
  • DEPICTER: Intrinsic Disorder and Disorder Function Prediction Server (uses 10 popular methods) (online)
  • MISTIC2: comprehensive server to study coevolution in protein families - circular dataviz (online)
  • CGDV: a webtool for circular visualization of genomics and transcriptomics data (online, still running?)
  • myCircos: a CIRCOS module for interactive protein sequence visualization - circular dataviz (genes) (online)
  • Circa: Intuitive software for creating circos plots - circular dataviz (genes) (standalone)
  • I-PV: a CIRCOS module for interactive protein sequence visualization (standalone)
  • Logomaker: beautiful sequence logos in Python (standalone)
  • Sourmash: Large-scale sequence comparisons (standalone)
  • SCOT: Rethinking the Classification of Secondary Structure Elements (standalone)
  • Kalign: multiple sequence alignment of large datasets (standalone)
  • Miew: 3D Molecular Viewer (standalone)
  • MAFFT-DASH: integrated protein sequence and structural alignment (online and standalone all OS)
  • Zebra2: Advanced and Easy-To-Use Web-Server for Bioinformatic Analysis of Subfamily-Specific and Conserved Positions in Diverse Protein Superfamilies (online)
  • GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters (online)
  • Phylogeny.fr: sequence searching, multiple sequence alignment, model selection, tree inference, tree drawing and a large panel of standard methods such as distance, parsimony, maximum likelihood and Bayesian (online)
  • PASTA 2.0: an improved server for protein aggregation prediction (online)
  • PSA: Pairwise (local) Sequence Alignment (EMBL-EBI) (online)
  • XSuLT: annotate an alignment with structural information in the form of formatting styles (online)
  • Prosat+ visualize 3D structure, sequences, fetch related sequence, (protein structure annotation online)
  • DeepIDP-2L: protein intrinsically disordered region prediction by combining convolutional attention network and hierarchical attention network (online)
  • MoRFpred: Predicting Functions of Disordered Proteins (online)
  • PTM-ssMP: Server for Predicting Different Types of Post-translational Modification Sites Using Novel Site-specific Modification Profile (online)
  • MAFFT (sequence alignment): (online)
  • iFeature: (a python package and web server for features extraction and selection from protein and peptide sequences) (online)
  • StructureMapper: a high-throughput algorithm for analyzing protein sequence locations in structural data (online)
  • BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra (online)
  • Psfpss: PredictSuperFam - PSS-3D1D (fold recognition server based on Protein Secondary Structure and 3D1D Profiles) (online)
  • MPI Bioinformatics Toolkit: one-stop web service for protein bioinformatic analysis (online)
  • Jabaws: multiple sequence alignment with Clustal Omega, Clustal W, MAFFT, MUSCLE, T-Coffee, ProbCons, MSAProbs, and GLProbs; prediction of protein disorder with DisEMBL, IUPred, Jronn, GlobPlot; calculation of amino acid alignment conservation with AACon (online and standalone)
  • PredictProtein: started out by predicting secondary structure and returning families of related proteins. Solvent accessibility and transmembrane helix prediction followed suit shortly thereafter (online)
  • PSSweb: structural statistics (online)
  • ConSurf: identification of functional regions, map conserved amino acids in 3D, conservation aa on sequences (online)
  • ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism (e.g, aa conservation… input PDB) (online)
  • KMAD: intrinsically disordered proteins (online)
  • PSI/TM-Coffee: Align Proteins using Homology Extension against Reduced Databases (online)
  • TCS: Evaluates your Alignment and outputs a Colored version indicating the local reliability (online)
  • AlignMe Membrane proteins. web server for alignment of membrane protein sequences (links to MutationExplorer...) (online and standalone)
  • Memoir: membrane proteins, homology modelling algorithm designed for membrane proteins. The inputs are the sequence which is to be modelled, and the 3D structure of a template membrane protein (online)
  • PconsC3 (accurate contact predictions) (online)
  • RFcon: predicting protein residue-residue contacts using random forests and deep networks (standalone and online)
  • PROMALS3D: multiple sequence and structure alignment server (online)
  • BlockLogo: input multiple seq alignment (online)
  • PRALINE: multiple sequence alignment (online)
  • Skylign: tool for creating logos representing both sequence alignments and profile hidden Markov models (generate logo) (online)
  • DIALIGN: multiple sequence alignment (online)
  • Seq2Logo: web-based sequence logo generation (online)
  • DALI 3D, sequence align, logo, service for comparing protein structures in 3D (online)
  • TopMatch-web: Pairwise matching of large assemblies of protein and nucleic acid chains in 3D (online)
  • FATCAT 2.0 server: Flexible protein structure alignment algorithm (online)
  • UniProt: protein database (online)
  • SIFTS: updated structure integration with function, taxonomy and sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins (eg map Uniprot to PDB) (online)
  • PDBsum: Pictorial database of 3D structures in the Protein Data Bank - (extra data on SARS-CoV-2 protein structures and AlphaFold models) (online)
  • PDBsum1: a standalone program for generating PDBsum analyses (standalone)
  • Protein-Sol: predict protein solubility from sequence (online)
  • Protter: interactive protein feature visualization (sequence view of a protein in 2D) (online)
  • WebLogo: application designed to make the generation of sequence logos easy and painless (online)
  • Rosetta ToxDock: ensemble-docking and extensive conformational sampling and many other modeling protocols like Sequence Tolerance Protocol ...(online)
  • SMART: Simple Modular Architecture Research Tool (online)

3D molecular visualization

  • IFPAggVis: Systematic analysis, aggregation and visualisation of interaction fingerprints for molecular dynamics simulation data (standalone)
  • VTX: High performance molecular visualization software (Windows, Linux) (standalone)
  • VTR: A Web Tool for Identifying Analogous Contacts on Protein Structures and Their Complexes (online)
  • Molstar: (Mol*) modern web-based open-source toolkit for visualisation and analysis of large-scale molecular data (online)
  • Proteopedia: Protein - Macromolecule dataviz - life in 3D (online)
  • Chimera: (standalone)
  • PyMolshortcuts: Shortcuts For Faster Image Creation in PyMOL - Scripts (standalone)
  • Pymol-script-repo: PyMol python scripts (standalone)
  • Nglviewer: view molecular 3D structures (online)
  • MichelaNGLO: An interactive protein on your website with a few clicks (standalone)
  • Voronoia 4-ever: enables fully automated analysis of the atomic packing density of macromolecules (online)
  • Aquaria: Simplifying insight from protein structures (online)
  • YASARA: molecular-graphics, -modeling and -simulation program (standalone)
  • MolArt: MOLecular STructure AnnotatoR, enables users to view annotated protein sequence (including variation data from large scale studies) and overlay the annotations over a corresponding experimental or predicted protein structure (standalone)
  • dr_Sasa: Calculation of accurate interatomic contact surface areas for the quantitative analysis of non-bonded molecular interactions (online and standalone)
  • Getarea: Calculation of Solvent Accessible Surface Areas, Atomic Solvation Energies and Their Gradients for Macromolecules (online)
  • VoroContacts: a tool for the analysis of interatomic contacts in macromolecular structures (online and standalone)
  • PyMOLProbity: The plugin allows a PyMOL user to produce MolProbity-style visualization of atomic interactions within a structure (e.g. H-bonds, van der Waals interactions and clashes) directly within a PyMOL session (standalone)
  • PyMod 3: an open source PyMOL plugin, designed to act as an interface between PyMOL and several bioinformatics tools (standalone)
  • Iris: interactive all-in-one graphical validation of 3D protein model (standalone)
  • POVME: binding pocket analysis software (standalone)
  • BlendMol: Advanced Macromolecular Visualization in Blender (standalone)
  • ezCADD: a Rapid 2D/3D Visualization Enabled Web Modeling Environment for Democratizing Computer-Aided Drug Design (small molecule docking, protein docking, 2D/3D interaction viz, de novo lead optimization, pocket search and polypharmacology) online
  • ChimeraX: molecular graphics (standalone)
  • SEQCROW: Quantum chemistry plugin for UCSF ChimeraX (standalone)
  • WebMO: free World Wide Web-based interface to computational chemistry packages (standalone)
  • INTAA: Amino Acid Interaction (INTAA) web server. Calculation of the residue Interaction Energy Matrix for any protein structure. Aims to identify key residues within protein structures which contribute significantly to the stability of the protein (online)
  • Protein Imager: 3D molecular structure display (online)
  • PyMol: molecular graphics (standalone)
  • 3D Protein Imaging: macromolecule figure generator (online)
  • OpenStructure: look at molecular structures (standalone)
  • PLIP : view protein-ligand non covalent interactions (standalone)
  • BINANA 2: Characterizing Receptor/Ligand Interactions in Python and JavaScript (standalone) or online (durrantlab.pitt.edu/binana/)
  • ProteinsPlus: prepare and analyze protein and ligands (online)
  • PLIP: protein-ligand non covalent interactions (online)
  • SAMSON: software for adaptative modeling and simulation (nano), GROMACS can be launched from SAMSON... (standalone)
  • ProteinVolume: calculating molecular van der Waals and void volumes in proteins (online)
  • VADAR: Volume, Area, Dihedral Angle Reporter.. is a compilation of more than 15 different algorithms and programs for analyzing and assessing peptide and protein structures from their PDB coordinate data (Ramachandran plot, surface area…) (online)
  • MoMA-LigPath: MoMA-LigPath is a web server simulating protein-ligand unbinding (online)
  • MOLEonline: provides a direct access to MOLE functionality and enables on-line and easy-to-use interactive channel analysis (online)
  • BetaCavityWeb: webserver which computes cavities for a given molecular structure and a given spherical probe, and reports their geometrical properties (online)
  • Ezmol: A wizard for protein display and image production (online)
  • QuteMol: (standalone)
  • ICM: (standalone)
  • iMolview: Molsoft molecular viewer for iPad and mobile phone (standalone)
  • CCP4: (standalone)
  • Swiss-PdbViewer -DeepView: (standalone)
  • cellPACK: biological software tool designed to assemble large scale models from molecular building-blocks (standalone)
  • cellVIEW: a Tool for Illustrative and Multi-Scale Rendering of Large Biomolecular Datasets (standalone)
  • Avogadro: advanced molecule editor and visualizer designed for cross-platform use (draw molecules...) (standalone)
  • MolView: draw and viewer in 2D or 3D of small molecules and proteins (online)
  • Aquaria simplifying the generation of insight from protein structures (online)
  • WebMolCS: server to visualize 3D Chemical Spaces (online and standalone)
  • Web3DMol: view protein in 3D and sequences (online)
  • RealityConvert (makes objects compatible for Augmented Reality and Virtual Reality and for 3D printing) (online and standalone)
  • VMD: molecular visualization program (standalone)
  • NAMD: a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. Simulation preparation, energy minimization... and analysis is integrated into the visualization package VMD (standalone)

3D structure prediction and validation : macromolecules
Homology Modeling & others

  • Assess: structure assessment web server for proteins, complexes and more (online, 2024).
  • DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction (online)
  • iQDeep: web server for protein scoring using multiscale deep learning models (evaluate quality of the 3D structure) (standalone)
  • AS2TS: system for protein structure modeling and analysis (online)
  • ModFlex: Towards Function Focused Protein Modeling (online)
  • Pras_Server: Protein Repair and Analysis Server: A Web Server to Repair PDB Structures, Add Missing Heavy Atoms and Hydrogen Atoms, and Assign Secondary Structures by Amide Interactions (online)
  • Pras_Server: Protein Repair and Analysis Server: A Web Server to Repair PDB Structures, Add Missing Heavy Atoms and Hydrogen Atoms, and Assign Secondary Structures by Amide Interactions (standalone)
  • LoopGrafter: a web tool for transplanting dynamical loops for protein engineering (online)
  • SWORD2: hierarchical analysis of protein 3D structures (Optimized Recognition of protein Domains) (online)
  • PDBFixer: application for fixing problems in PDB - Protein Data Bank files, missing residues, loop... (standalone)
  • FALCON2: a web server for high-quality prediction of protein tertiary structures (online)
  • GPU-I-TASSER: a GPU accelerated I-TASSER protein structure prediction tool (standalone)
  • HOMELETTE: a unified interface to homology modelling software (standalone)
  • ProFitFun: a protein tertiary structure fitness function for quantifying the accuracies of model structures (standalone)
  • XEFoldmine: Interpreting a black box predictor to gain insights into early folding mechanisms (online)
  • MoMA-LoopSampler: A web server to exhaustively sample protein loop conformations (online)
  • MULTICOM: Protein Structure Prediction Server Empowered by Deep Learning and Contact Distance Prediction (online)
  • AlphaFold: Protein Structure Database (predicted human 3D proteins, July 2021)
  • AlphaFlow: AlphaFold Meets Flow Matching for Generating Protein Ensembles (protein flexibility) (standalone, 2024)
  • ESMFold: ESM Metagenomic Atlas contains several millions of predicted protein structures (can be used via ChimeraX) (online)
  • ESM: Evolutionary Scale Modeling to predict protein 3D structure (standalone) (online)
  • ColabFold: making protein folding accessible to all (standalone)
  • AlphaFold-Multimer: a model that can predict the structure of multi-chain protein complexes with increased accuracy (standalone)
  • UFold: fast and accurate RNA secondary structure prediction with deep learning (online and standalone via github.com)
  • rna-tools.online: a Swiss army knife for RNA 3D structure modeling workflow (online)
  • Openfold: A faithful PyTorch reproduction of DeepMind's AlphaFold2 (standalone)
  • ProFOLD: CopulaNet: Learning residue co-evolution directly from multiple sequence alignment for protein structure prediction (standalone)
  • RNA-MoIP: Modeling and Predicting RNA Three-Dimensional Structures (online)
  • vfold3D2: Predicting RNA Scaffolds with a Hybrid Method of Vfold3D and VfoldLA (online)
  • Vfold-Pipeline: RNA 3D structure prediction from sequences (online)
  • OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures (online)
  • ReFOLD3: refinement of 3D protein models with gradual restraints based on predicted local quality and residue contacts (online)
  • DeepRefiner: high-accuracy protein structure refinement by deep network calibration (online)
  • Shape: Similarity searching enables real-time retrieval of proteins resembling a query target, from a PDB input, together with resulting alignments (online)
  • Caretta: A multiple protein structure alignment and feature extraction suite (standalone)
  • ProMod3: A versatile homology modelling toolbox (standalone, the online version is for instance at the SWISS-MODEL web-server) (standalone)
  • VGGfold: Why can deep convolutional neural networks improve protein fold recognition (input sequence) (online)
  • TopSuite Web Server: A Meta-Suite for Deep-Learning-Based Protein Structure and Quality Prediction (online)
  • PRosettaC: Rosetta based modeling of PROTAC mediated ternary complexes (online)
  • Iris: interactive all-in-one graphical validation of 3D protein model (standalone)
  • MODalign: display & check and improve alignments (online)
  • DEMO: method for automated assembly of full-length structural models of multi-domain proteins (online)
  • ITScorePro: Statistical mechanics-based energy scoring function for structural model selection in protein structure prediction (standalone)
  • FASPR: An Open-Source Tool for Fast and Accurate Protein Side-Chain Packing (standalone on github and online)
  • AWSEM-Suite: A Protein Structure Prediction Server Based on Template-Guided, Coevolutionary-Enhanced Optimized Folding Landscapes. Predicting monomeric protein tertiary structures when a suitable structure template is not available (folding) (online)
  • PDBexplorer: Web application for the interactive visualization of chemical space of the Protein Data Bank (PDB) characterized by protein shape fingerprint (3DP) and shape similarity (online)
  • MADOKA: an ultra-fast approach for large-scale protein structure similarity searching (online)
  • Multifoxs: Multi-state modeling with SAXS profiles (online)
  • eModel-BDB: database of comparative structure models of drug-target interactions from the Binding Database (database online)
  • CATHER: a novel threading algorithm with predicted contacts (online)
  • HUMMOD: Homology modeling (a database of all available human homology models can also be found) (online and database)
  • CAMEO: continuously evaluate the accuracy and reliability of predictions (online)
  • Robetta: protein structure prediction service (homology modeling and ab initio fragment assembly) (online)
  • C-QUARK: template-less protein structure prediction (online)
  • C-I-TASSER: template-less protein structure prediction (online)
  • trRosetta: template-less protein structure prediction (online)
  • GREMLIN Database: precomputed models using Rosetta/Gremlin (online)
  • Modelsearch : Search protein sequence in databases of 3D precomputed models (online)
  • CABS-FOLD: de novo modeling, can also use alternative templates (consensus modeling) (online)
  • DeepFR: Remote template selection, 3D modeling, ab initio (online)
  • Integrative Modeling Platform (IMP): Modeling Biological Complexes Using Integrative Modeling Platform (online)
  • ValTrendsDB: bringing Protein Data Bank validation information closer to the user (online)
  • PSICA: a fast and accurate web service for protein model quality analysis (online)
  • DaReUS-Loop: a web server to model multiple loops in homology models (online)
  • Yosshi: web-server for disulfide engineering by bioinformatic analysis of diverse protein families (biologics, online)
  • Protein Folding via deep learning: End-to-End Differentiable Learning of Protein Structure (standalone)
  • IntFOLD: unified resource for the automated prediction of: protein tertiary structures with built-in estimates of model accuracy (EMA), protein structural domain boundaries, natively unstructured or disordered regions in proteins, and protein-ligand interactions (online)
  • VoroMQA: assessing three-dimensional structures of proteins and protein complexes (online)
  • INGA 2.0: improving protein function prediction for the dark proteome (can process entire genomes) (online)
  • GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein model structure (online)
  • KORP: Knowledge-based 6D potential for fast protein and loop modeling (online)
  • Ornate: Protein model quality assessment using 3D oriented convolutional neural networks (standalone)
  • TOPOLINK: A package to evaluate structural models using chemical crosslinking distance constraints (standalone and online)
  • HMMER: biosequence analysis using profile hidden Markov models (standalone)
  • HMMER: (online)
  • TCRmodel: high resolution modeling of T cell receptors from sequence (online)
  • GapRepairer: server to model a structural gap and validate it using topological analysis (loop, linker...) (online)
  • Mustguseal: Multiple Structure-Guided Sequence Alignment of Protein Families (online)
  • PREFMD: protein structure refinement via molecular dynamics simulations. Standalone scripts also available (online)
  • SuperLooper2: insertion of missing segments such as loops in proteins (SL2) (online)
  • LoopSampler: tool to investigate loop structures (online)
  • SwissModel: fully automated protein structure homology-modelling server (pages dedicated to Covid-19) (online)
  • DisCovER: distance-based covariational threading for weakly homologous proteins (standalone)
  • I-TASSER: (Iterative Threading ASSEmbly Refinement) is a hierarchical approach to protein structure and function prediction. It first identifies structural templates from the PDB by multiple threading approach LOMETS, with full-length atomic models constructed by iterative template fragment assembly simulations (online)
  • HHpred: homology and structure prediction (online)
  • ModWeb: A Server for Protein Structure Modeling, Sali's lab (online)
  • EVfold: uses evolutionary variation. Explore a set of ranked predicted 3D structure models (online)
  • PyMod: homology modeling with PyMOL possible (standalone)
  • 3D-DART: a DNA structure modelling server (online)
  • ORION: sensivitve method for protein template detection (Optimized protein fold RecognitION) (online)
  • Phyre2: Protein Homology/analogY Recognition Engine (online)
  • FoldTR: Improving protein fold recognition using triplet network and ensemble deep learning (online)
  • SPARKSX: fold recognition (online)
  • ESyPred3D: automated homology modeling program (online)
  • QUARK ab initio protein folding (online)
  • MEMOIR membrane protein modeling (online)
  • (PS)2-v2: Protein Structure Prediction Server (online)
  • RaptorX: a Web Portal for Protein Structure and Function Prediction (online)
  • BHAGEERATH-H: A Homology ab-intio Hybrid Web server for Protein Tertiary Structure Prediction (online)
  • 3D-JIGSAW: protein modeling (online)
  • FUGUE: Sequence-structure homology recognition (standalone and online(
  • Protein Model Portal (PMP): gives access to various models computed by comparative modeling methods provided by different partner sites (online)
  • GENO3D: automatic modeling of proteins three-dimensional structure online)
  • LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins (template-based protein structure prediction) (online)
  • HOMCOS: HOMology modeling of COmplex Structure (online)
  • ProFold: web server for protein fold classification (online)
  • PRIMO: PRotein Interactive MOdeling (online)
  • ModPipe: a completely automated software pipeline that can calculate protein structure models for a large number of sequences with almost no manual intervention (online)
  • RaptorX-Contact Map: predicts contact map of a protein sequence without using any templates. It applies an ultra-deep learning model to predict contacts and works particularly well on proteins without many sequence homologs (online)
  • HotSPOT Wizard: design mutations
  • Selecton: Server for the Identification of Site-Specific Positive Selection & Purifying Selection (online)
  • Matras: 3D Structure Comparison (online)
  • PDBeFold: 3D Structure Comparison (online)
  • Dali: 3D Structure Comparison (online)
  • PELE: Protein Energy Landscape Exploration, Localized perturbation, Side chain sampling, Minimization. Identify functional tunnels based on the profile of potential energies of binding and unbinding trajectories (online)
  • Several sequence alignment list of tools (online)
  • PDBparam: computing several parameters from three dimensional structures of proteins, descriptors for machine learning (online)
  • MolProbity (Validation of 3D structures) (online)
  • Validation HElper for LIgands and Binding Sites (standalone) (VHELIBS)
  • PROCHECK (Validation of 3D structures) (standalone) (online via PDBsum)
  • PSVS: server for analysis of 3D protein structure (includes PROCHECK, ramachandran plot...and many others) (online)
  • ProSA-Web: protein structure analysis (needs a PD ID as input no upload) (online)
  • Anolea: Atomic Non-Local Environment Assessment (online)
  • VADAR (Validation of 3D structures) (online)
  • ProTSAV (Validation of 3D structures, meta-server) (standalone and online)
  • ModFOLD: Validation of 3D structures, May 2021, new ModFOLD8 version (accurate global and local quality estimates for 3D protein models) (online)
  • VLDPws (Validation of 3D structures) (online)
  • PDB_REDO (Validation of 3D structures, ligands-pockets) (online)
  • ProQ2 (Validation of 3D structures) (online)
  • ProQ3 (Validation of 3D structures) (online)
  • QMEAN (Validation of 3D structures) (standalone and online)
  • Verify3D (Validation of 3D structures) (online)
  • dDFIRE (Validation of 3D structures) (online)
  • Errat (Validation of 3D structures) (online)
  • 3DBIONOTES: automatically annotate biochemical and biomedical information onto structural models. Current sources of information include post-translational modifications, genomic variations associated to diseases, short linear motifs, immune epitopes sites, disordered regions and domain families (online)
  • 3DBionotes COVID-19 Edition: integrates multiple Web Services and an interactive Web Viewer to provide a unified environment in which biological annotations can be analyzed in their structural context (online)
  • Bio3D-web: built on top of the Bio3D package, for the investigation of protein structure ensembles (not running but the standalone is available) (online)
  • Molstack: visualization and analysis of electron density data (online)
  • CheckMyBlob: Recognizing and validating ligands (electron density map and related) (online)

Glycomics, carbohydrates and glycobiology research

  • GlycoSHIELD-MD: simple MD pipeline to generate realistic glycoprotein models (online, 2024).
  • PCA-pred: Protein-Carbohydrate complex binding Affinity Prediction (online)
  • Glycowork: A Python package for glycan data science and machine learning (including GlycoDraw for high-quality glycan figures) (standalone)
  • CAZy: The carbohydrate-active enzyme database (online database)
  • O-GlcNAc: The O-GlcNAc database (online)
  • GLYCO: a tool to quantify glycan shielding of glycosylated proteins (standalone)
  • CSM-carbohydrate: protein-carbohydrate binding affinity prediction and docking scoring function (online)
  • GLYCAM-Web: 3D prediction of carbohydrates and proteins-carbohydrates (online)
  • CHARMM-GUI Glycan Modeler: Modeling and Simulation of Carbohydrates and Glycoconjugates (online)
  • DrawGlycan-SNFG & gpAnnotate: Rendering glycans and annotating glycopeptide mass spectra (standalone and online)
  • GlycoMine_Struct: Highly accurate mapping of the human N-linked and O-linked glycoproteomes (online)
  • Glycosylator: a Python framework for the rapid modeling of glycans (standalone)
  • SugarBindDB: provides information on known carbohydrate sequences to which pathogenic organisms (bacteria, toxins and viruses) specifically adhere (online)...ExPASy
  • GlyConnect: platform integrating sources of information to help characterise the molecular components of protein glycosylation...ExPASy (online)
  • ExPASy: Glycomics resources eg: SugarSketcher... (online)
  • REStLESS: Automated Translation of Glycan Sequences from Residue-Based Notation to SMILES and Atomic Coordinates (online)
  • UniLectin3D: a database of carbohydrate binding proteins (online)
  • Glycomics@ExPASy: glycoinformatics (online)
  • UniCarbKB: online information storage and search platform for glycomics, carbohydrates and glycobiology research (online)
  • dbSWEET: An Integrated Resource for SWEET Superfamily to Understand, Analyze and Predict the Function of Sugar Transporters in Prokaryotes and Eukaryotes (online)
  • Glycosciences.de: databases and bioinformatics tools for glycobiology, carbohydrates and glycomics (online)
  • Glyco3D: a portal for structural glycosciences, glycobiology, carbohydrates (online)

Antibody modeling and related (eg., vaccine)

  • AntPack: antibody sequence generative modeling, mixture models may be all you need (Antibody numbering, Humanness and developability) (standalone, 2024)
  • AbFlex: Designing antibody complementarity determining regions with flexible CDR definition (equivariant graph neural network model) (standalone, 2024)
  • AB-Amy: machine learning aided amyloidogenic risk prediction of therapeutic antibody light chains (standalone)
  • DG-Affinity: predicting antigen-antibody affinity with language models from sequences (online)
  • ADCdb: the database of antibody–drug conjugates (online)
  • ARMADiLLO: server for analyzing antibody mutation probabilities (online)
  • TCRmodel2: High-resolution modelling of T cell receptor recognition (online)
  • SEPPA-mAb: Spatial epitope prediction of protein antigens for monoclonal antibodies (online)
  • xProtCAS: Toolkit for Extracting Conserved Accessible Surfaces from Protein Structures (interaction with other biomolecules) (standalone)
  • xProtCAS: Toolkit for Extracting Conserved Accessible Surfaces from Protein Structures (interaction with other biomolecules) (online)
  • Vaxi-DL: a predictive system that uses Deep Learning algorithms to classify given protein sequences into vaccine candidates or the non-vaccine candidates (online)
  • AREA-AFFINITY: Server for Machine Learning-Based Prediction of Protein-Protein and Antibody-Protein Antigen Binding Affinities (online)
  • ClusPro-AbEMap: prediction of antibody epitopes (online)
  • CamSol: Automated optimisation of solubility and conformational stability of antibodies and proteins (online)
  • epitope1D: Accurate taxonomy-aware B-cell linear epitope prediction (online)
  • GraphBepi: Identifying B-cell epitopes using AlphaFold2 predicted structures and pretrained language model (online)
  • BepiPred-3.0: Improved B-cell epitope prediction using protein language models (online)
  • The Antibody Registry: Ten years of registering antibodies (online)
  • PITHA: A Webtool to Predict Immunogenicity for Humanized and Fully Human Therapeutic Antibodies (online)
  • AbCPE: Antibody Class(es) Predictor for Epitopes (online)
  • INDI: integrated nanobody database for immunoinformatics (online)
  • ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction (for now trained for detecting protein–protein and protein–antibody binding sites) (online)
  • ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction (for now trained for detecting protein–protein and protein–antibody binding sites) (standalone)
  • Epitope-Evaluator: An interactive web application to study predicted T-cell epitopes (online)
  • SAbDab: SAbDab in the age of biotherapeutics: updates including SAbDab-nano (online)
  • AllerCatPro 2.0: a web server for predicting protein allergenicity potential (online)
  • SSH2.0: A Better Tool for Predicting the Hydrophobic Interaction Risk of Monoclonal Antibody (online)
  • BCEPS: A Web Server to Predict Linear B Cell Epitopes with Enhanced Immunogenicity and Cross-Reactivity (online)
  • np_epitope_predictor: prediction of non-peptidic epitopes (online)
  • PixelDB: the Peptide Exosite Location Database, compiles 1966 non-redundant, high-resolution structures of protein-peptide complexes filtered to minimize the impact of crystal packing on peptide conformation (dataset)
  • ProtPepRFScorePaper2021: RF models and selected data. Protein-peptide RF re-scoring (standalone)
  • Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning (online)
  • VirVACPRED: A Web Server for Prediction of Protective Viral Antigens (online)
  • EpiSurf: metadata-driven search server for analyzing amino acid changes within epitopes of SARS-CoV-2 and other viral species (Covid-19) (GenBank and COG-UK sequences) (online)
  • EpiSurf: metadata-driven search server for analyzing amino acid changes within epitopes of SARS-CoV-2 and other viral species (Covid-19) (GISAID sequences) (online)
  • DLAB: Deep learning methods for structure-based virtual screening of antibodies (standalone)
  • AbYBank: antibody-antigen 3D structures (database online)
  • CoV3D: A resource for structures of coronavirus proteins and their recognition by antibodies and other molecules (Covid-19) (online)
  • CoV-AbDab: Coronavirus-Binding Antibody Sequences & Structures (Covid-19) (online)
  • ViPR: An open bioinformatics database and analysis resource for virology study (can be used for Covid-19) (online)
  • IEDB-AR: Epitope Prediction and Analysis Tools from IEBD (can be used for Covid-19) (online)
  • Epitome: a database of all known antigenic residues and the antibodies that interact with them (online)
  • IMGT: The global ImMunoGeneTics Web Resource for immunoglobulins (IG), T cell receptors (TR), major histocompatibility (MH) and related proteins of the immune system (RPI) (online)
  • MMDB: Biggest database of antibody, HLA and TCR crystallography structures (online)
  • AntiJen: a database containing quantitative binding data for peptides binding to MHC Ligand, TCR-MHC Complexes, T Cell Epitope, TAP , B Cell Epitope molecules and immunological Protein-Protein interactions (online)
  • HaptenDB: low molecular weight molecules which by itself do not elicit immune response until and unless complexed with an immunogenic carrier, such as protein
  • SACS: Summary of Antibody Structures in the Protein Databank, automatically updated each month (online)
  • COVID-19 Docking Server: An interactive server for docking small molecules, peptides and antibodies against potential targets of COVID-19 (online)
  • mmCSM-AB: Guiding Rational Antibody Engineering Through Multiple Point Mutations (online)
  • SAbPred: Structural Antibody Prediction Server (online)
  • mCSM-AB2: rapid analysis of both individual mutations or the entire binding interface to guide rational antibody affinity maturation (online)
  • EvoEF2: accurate and fast energy function for computational protein design (de novo sequence design on a given fixed protein backbone (standalone)
  • Thera-SAbDab: the Therapeutic Structural Antibody Database (online)
  • AbLIFT: Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces (online)
  • PROSS: Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability (protein-stability design, seldom introduce mutation in the core..check AbLIFT for mAb) (online)
  • mCSM-AB2: Guiding Rational Antibody Design Using Graph-Based Signatures. Web server providing rapid analysis of both individual mutations or the entire binding interface to guide rational antibody affinity maturation (online)
  • ProtaBank: provides a central repository for researchers to store, query, analyze, and share all types of protein engineering data (including antibodies, mAbs). Explore the impact of protein mutations (online)
  • OptMAVEn_2.0 and HUMANIZER: tools (affinity and more humanized sequences) for antibody design (standalone)
  • abYsis: A fully integrated antibody discovery system (online)
  • ABCD database: a repository for chemically defined antibodies (online)
  • Yvis: antibody high-density alignment visualization and analysis platform with an integrated database (online)
  • AppA: analysis, comparison, and visualization of contact residues and interfacial waters of antibody-antigen structures and models (online)
  • AbPredict 2: a server for accurate and unstrained structure prediction of antibody variable domains (online)
  • AbDesigner3D: a structure-guided tool for peptide-based antibody production (online)
  • BRepertoire: a user-friendly web server for analysing antibody repertoire data (online)
  • Rosetta Antibody (online)
  • PIGSpro: automatic modeling of immunoglobulin variable domains (online)
  • SmrtMolAntibody: commercial tool
  • Tabhu: AntiBody Humanization (online)
  • PIGSPro: prediction of Ab structures (online)
  • AAgAtlas: Human autoantigens (database with their associated diseases) (online)
  • TABS: Therapeutic Antibody Database (online)
  • AnkPlex: refinement of near-native ankyrin-protein docking, protein used to replace antibodies (online)

GPCR modeling

  • pdCSM-GPCR: predicting potent GPCR ligands with graph-based signatures, ligand-based (online)
  • GPCRana: quantitative analysis of GPCR structures (online)
  • RosettaGPCRPocketSize: Improving the Modeling of Extracellular Ligand Binding Pockets (standalone)
  • PRECOGx: exploring GPCR signaling mechanisms with deep protein representations (online)
  • GGIP: A Web Server for GPCR-GPCR Interaction Pair Prediction (online)
  • GPCRdb 2021: adding GPCR structure models and ligands (online)
  • GRIP: interface prediction of GPCRs (online)
  • HomolWat: Incorporates Homologous Water Molecules Into GPCR Structures (online)
  • WDL-RF :Predicting Bioactivities of Ligand Molecules Acting with G Protein-coupled Receptors by Combining Weighted Deep Learning and Random Forest (online)
  • GPCRmd: comprehensive database and web platform for MD simulations of GPCRs and related analysis including dataviz (online)
  • GPCR-SSFE :fragment-based molecular modeling web tool for Class A G-protein coupled receptors (online)
  • GPCR-SSFE: including Snake-like-Plot for GPCRs (online)
  • Galaxy7TM :flexible GPCR-ligand docking by structure refinement (improves an input GPCR structure by simultaneous ligand docking and flexible structure refinement using GALAXY methods) (online)
  • GPCR-ModSim :A comprehensive web based solution for modeling G-protein coupled receptors (online)
  • ModRefiner :algorithm for atomic-level, high-resolution protein structure refinement (online)
  • GPCRM: A web service to predict structures of G-protein-coupled receptors (GPCRs) using advanced homology modeling tools (online)
  • GPCR-I-TASSER: computational method designed for 3D structure prediction of G protein-coupled receptors (online)
  • GPCRautomodel: Automatic Modeling of G-Protein Coupled Receptors based on Fold Recognition Techniques: Application to Mammalian Olfactory Receptors (online)
  • GOMoDo: A GPCRs Online Modeling and Docking Webserver (online)
  • pyGOMoDo: GPCRs modeling and docking with python (standalone)

Protein-protein docking

  • FoldDock: simultaneous folding and docking protocol FoldDock and AlphaFold (standalone)
  • AREA-AFFINITY: Server for Machine Learning-Based Prediction of Protein-Protein and Antibody-Protein Antigen Binding Affinities (online)
  • LightDock: Artificial Intelligence-powered modeling of macromolecular interactions (macromolecular docking framework, online)
  • SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions (PPI) (online) (or http://sbi.upf.edu/spserver/)
  • DockSurf: A molecular modeling software for the prediction of protein/surface adhesion (eg. gold surfaces) (online)
  • pyDockDNA: A new web server for energy-based protein-DNA docking and scoring (online)
  • GalaxyDomDock: An Ab Initio Domain-domain Docking Web Server for Multi-domain Protein Structure Prediction (online)
  • PPI-Affinity: Prediction and Optimization of Protein-Peptide and Protein-Protein Binding Affinity (online)
  • DeepComplex: A Web Server of Predicting Protein Complex Structures by Deep Learning Inter-chain Contact Prediction and Distance-Based Modelling (online)
  • GraphPPIS: Structure-aware protein-protein interaction site prediction using deep graph convolutional network (online), standalone on github
  • InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps (online)
  • pyDock : structural prediction of protein-protein interactions (online)
  • HMI-PRED: A Web Server for Structural Prediction of Host-Microbe Interactions Based on Interface Mimicry (online)
  • ClusPro TBM: Toward combining template-based methods with free docking (protein-protein docking) (online)
  • pyDockEneRes: per-residue decomposition of protein-protein docking energy (online)
  • PIIMS: Mutation Hotspot Scanning at the Protein-Protein Interface (online)
  • BAlaS: fast, interactive and accessible computational alanine-scanning using BudeAlaScan (online)
  • DOVE: convolutional deep neural network-based approach named DOcking decoy selection with Voxel-based deep neural nEtwork (DOVE) for evaluating protein docking models (online)
  • EROS-DOCK: protein–protein docking using exhaustive branch-and-bound rotational search (standalone)
  • IRaPPA: pyDockRescoring Server (online)
  • PRODIGY-crystal: classification of biological interfaces in protein complexes (online)
  • INTERSPIA: Explore the Dynamics of Protein-Protein Interactions Among Multiple Species (online)
  • HawkDock: to predict and analyze the protein-protein complex based on computational docking and MM/GBSA (online)
  • CoDockPP: A Multistage Approach for Global and Site-Specific Protein-Protein Docking (online)
  • InterPred: A pipeline to identify and model protein-protein interactions (online)
  • GalaxyTongDock: Symmetric and asymmetric ab initio protein-protein docking web server with improved energy parameters (online)
  • ezCADD: a Rapid 2D/3D Visualization Enabled Web Modeling Environment for Democratizing Computer-Aided Drug Design (small molecule docking, protein docking, 2D/3D interaction viz, de novo lead optimization, pocket search and polypharmacology) online
  • ClusPro FMFT-SAXS: Ultra-fast Filtering Using Small-Angle X-ray Scattering Data in Protein Docking (online and standalone)
  • RosettaDock: Efficient Flexible Backbone Protein-Protein Docking for Challenging Targets (standalone and online)
  • QASDOM: Quality ASsessment of DOcking Models, protein-protein (online)
  • DockQ: A Quality Measure for Protein-Protein Docking Models (standalone)
  • Dockground: A comprehensive data resource for modeling of protein complexes, datasets, decoys... (online)
  • LightDock: a new multi-scale approach to protein-protein docking (standalone)
  • (PS)2: Protein Structure Prediction Server (can be used for complexes) (online)
  • Memdock: alpha-helical membrane protein docking algorithm (online)
  • DOCKSCORE: rank docked poses (online)
  • DockStar: Modelling of multimolecular protein complexes (online)
  • FiltRest3D: filter predicted models (online)
  • InterEvDock2: protein docking using evolutionary and biological information from homology models and multimeric inputs (online)
  • webSDA: Simulation of Diffusional Assosiation (SDA) (online)
  • AIDA: Ab Initio Domain Assembly Server (online)
  • FiberDock, FireDock, FlexDock, PatchDock (online)...
  • FRODOCK: Fast Rotational DOCKing (online)
  • DOCK/PIERR: Protein Docking Server (online)
  • ZDOCK: docking (online)
  • PRISM: PRotein Interactions by Structural Matching (online)
  • SwarmDock: webservice for generating 3D structures of protein-protein complexes (online)
  • 3D-Garden: A system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm (online)
  • GRAMM: Protein-Protein Docking Web Server (online)
  • Haddock: High Ambiguity Driven protein-protein DOCKing (online requires login)
  • Cluspro: protein docking (online)
  • ClusPro-DC: discrimination between Xray and biological dimers (online requires login)
  • DisVis: visualizes the accessible interaction space (online)
  • GalaxyRefineComplex: Protein-protein complex structures generated by protein-protein docking methods can be refined (online)
  • PRODIGY: PROtein binDIng enerGY prediction (online)
  • Arpeggio: A webserver for calculating interatomic interactions in protein structures (online & standalone)
  • GWIDD: genome wide docking database (online)
  • P3DOCK: a protein-RNA docking webserver based on template-based and template-free docking (online)
  • GalaxyHomomer: protein homo-oligomer structure prediction from a monomer sequence or structure (online)
  • HDOCK: hybrid protein–protein and protein–DNA/RNA docking, Pushing the accuracy limit of shape complementarity for protein-protein docking (online)

Protein-protein pairwise predictions, networks, pathways

  • PPI3D: server for searching, analyzing and modeling protein-protein, protein-peptide and protein-nucleic acid interactions (online, 2024).
  • DF-PPI: Prediction of protein-protein interactions based on integrating deep learning and feature fusion (standalone, 2024).
  • ProInterVal: Validation of Protein–Protein Interfaces through Learned Interface Representations (standalone)
  • B4PPI: Pitfalls of machine learning models for protein-protein interaction networks (standalone)
  • PeSTo: parameter-free geometric deep learning for accurate prediction of protein binding interfaces (standalone)
  • PeSTo: parameter-free geometric deep learning for accurate prediction of protein binding interfaces (online)
  • FuzPred: offers insights into the structural and dynamical changes of proteins upon interactions (sequence-based prediction of the context-dependent binding modes of proteins) (online)
  • E2EDA: Protein Domain Assembly Based on End-to-End Deep Learning (online)
  • Ensemppis: A Transformer-Based Ensemble Framework for the Prediction of Protein-Protein Interaction Sites (online)
  • PPI-Miner: a PPI search pipeline for proteins containing specific substructure motif (3D) or sequence motif (2D). Besides discovering PPIs, PPI-Miner can also be used to help design molecular glues and protein vaccines (online)
  • PPI-Miner: a PPI search pipeline for proteins containing specific substructure motif (3D) or sequence motif (2D). Besides discovering PPIs, PPI-Miner can also be used to help design molecular glues and protein vaccines (standalone)
  • PRO-Simat: Protein network simulation and design tool (online)
  • iRefWeb: Navigating the Global Protein-Protein Interaction Landscape (online)
  • DeepBSRPred: deep learning-based binding site residue prediction for protein-protein interactions (standalone)
  • konnect2prot: A web application to explore the protein properties in a functional protein-protein interaction network (online)
  • CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning (PPI and regular binding sites) (online)
  • TOUGH-M1: A non-redundant and representative dataset of ligand-binding pockets extracted from proteins with globally unrelated sequences and structures (database)
  • FPocketWeb: protein pocket hunting in a web browser (online - standalone)
  • FTMove: Detection and Analysis of Cryptic and Allosteric Binding Sites by Mapping Multiple Protein Structures (online)
  • BIPSPI+: Mining Type-Specific Datasets of Protein Complexes to Improve Protein Binding Site Prediction (data set) (online)
  • INTACT: Molecular Interaction Database (PPI) (online)
  • IID: Informed Use of Protein–Protein Interaction Data: A Focus on the Integrated Interactions Database (IID) (tissue specific PPI networks across species) (online database)
  • SARS: Web interface for 3D visualization and analysis of SARS-CoV-2-human mimicry and interactions (Covid-19) (online)
  • STRING: Protein-Protein Interaction Networks (PPI) (online)
  • STITCH: Chemical-Protein Interaction Networks (PPI) (online)
  • I2D: Integrated Interactions Database is the first database providing tissue-specific protein-protein interactions (PPIs) for model organisms and human (online)
  • Proteo3Dnet: a web server for the integration of structural information with interactomics data (online)
  • CoVex: CoronaVirus Explorer, network and systems medicine web platform that integrates experimental virus-human protein interactions - COVID-19 (database online)
  • P-HIPSTer: a virus–host protein–protein interaction resource - COVID-19 (database online)
  • Wiki-CORONA: Search for PPIs related to Coronavirus Infection (COVID-19) (online)
  • PINOT: An Intuitive Resource for Integrating Protein-Protein Interactions (PPI network) (online)
  • CyTargetLinker: Extend biological networks (eg disease network with Chembl or drugbank compounds) in Cytoscape (standalone)
  • DOMMINO 2.0: a structural Database Of Macro-Molecular INteractiOns (online)
  • ProtDCal-Suite: numerical codification and functional analysis of proteins. Set of machine learning-based methods for studying proteins, PPI-Detect for PPI and protein-peptides... (online)
  • The OncoPPi Portal: an integrative resource to explore and prioritize protein-protein interactions for cancer target discovery (online)
  • Intersppiv2: A machine learning-based predictor of human-bacteria protein-protein interactions by incorporating comprehensive host network properties (online)
  • PPI disease pathways: Large-scale analysis of disease pathways in the human interactome (datasets, standalone, also available at marinkaz / pathways on GitHub)
  • Interactome INSIDER: a structural interactome browser for genomic studies, look at mutations (via HGMD, ClinVar, COSMIC) (online and standalone)
  • MEGADOCK-Web: an integrated database of high-throughput structure-based predicted protein-protein complexes (online)
  • HPID: human protein interaction database (online)
  • WebPropagate: a web-server for network propagation on PPI networks (online)
  • BIANA: Biologic Interaction and Network Analysis (standalone)
  • BIPS: Biana Interolog Prediction Server (online)
  • BioGRID: Biological General Repository for Interaction Datasets (online)
  • Consensuspathdb: integrates interaction networks in Homo sapiens including binary and complex protein-protein, genetic, metabolic, signaling, gene regulatory and drug-target interactions, as well as biochemical pathways (online)
  • Complex Portal: a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms (online)
  • LENS: Enrichment and network studies of proteins (online)
  • DT-Web: DT-Web: a web-based application for drug-target interaction and drug combination prediction through domain-tuned network-based inference (periodically synchronized with DrugBank and PathwayCommons) (online)
  • PPI3D: search, analyze and model protein-protein interactions in the context of 3D structures (online)
  • PluriPred: web server for predicting proteins responsible for pluripotency (online)
  • Deathbase: Cell Death Processes and Pathways (online)
  • ApoCanD: Database of Human Apoptotic Proteins in the context of cancer
  • PROFEAT: computing commonly used proteins features from amino acid sequence, and interaction network properties from network structure (online)
  • PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data (online)
  • HIPPIE: web tool to generate reliable and meaningful human protein-protein interaction networks (online)

Protein-protein binding region predictions and analysis

  • PITHIA: Protein Interaction Site Prediction Using Multiple Sequence Alignments and Attention (online)
  • DeepUMQA3: a web server for accurate assessment of interface residue accuracy in protein complexes (online)
  • HISNAPI: a bioinformatic tool for dynamic hot spot analysis in nucleic acid-protein interface with a case study (applied to SARS-CoV-2 RNA-dependent RNA polymerase, COVID-19) (online)
  • PEPPI: protein-protein interaction predictions (online)
  • ProtCAD: a comprehensive structural resource of protein complexes (online)
  • ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction (for now trained for detecting protein–protein and protein–antibody binding sites) (online)
  • ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction (for now trained for detecting protein–protein and protein–antibody binding sites) (standalone)
  • QSalignWeb: A Server to Predict and Analyze Protein Quaternary Structure (online)
  • INDEEP: 3D fully convolutional neural networks to assist in silico drug design on protein-protein interactions (standalone)
  • INTERCAAT: identifying interface residues between macromolecules (standalone)
  • Co-Var: Co-evolutionary landscape at the interface and non-interface regions of protein-protein interaction complexes (online)
  • RBinds: A user-friendly server for RNA binding site prediction (online)
  • VoroCNN: Deep convolutional neural network built on 3D Voronoi tessellation of protein structures (can identify protein interfaces)(standalone)
  • DELPHI: DEep Learning Prediction of Highly probable protein Interaction sites (uses sequence as input) (online)
  • PINA 3.0: mining cancer interactome (online)
  • PROFisis: machine learning-based method that identifies interacting residues from sequence alone (online)
  • PCPIP: Classification and prediction of protein-protein interaction interface using machine learning algorithm (online)
  • Cocomaps: bioCOmplexes COntact MAPS analyse and visualize the interface in biological complexes via intermolecular contact maps (online)
  • SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions (PPI) (online) (or http://sbi.upf.edu/spserver/)
  • LZerD: webserver for pairwise and multiple protein–protein docking (now Enhanced With de novo Structure Prediction) (online)
  • SPPIDER: identification of residues involved in protein-protein interactions (online)
  • ISPRED4: predicts protein-protein interaction sites starting from protein structure (online)
  • Fragment Hotspot Maps: Identifying the interactions that determine fragment binding at protein hotspots (online)
  • Hotspots API: A Python Package for the Detection of Small Molecule Binding Hotspots and Application to Structure-Based Drug Design (fragment mapping) (standalone)
  • PPISP: Protein–protein interaction site prediction through combining local and global features with deep neural networks (online)
  • MAPPIS: Multiple Alignment of Protein-Protein InterfaceS (PPIs) (online)
  • PCRPi: Integrates diverse metrics into a unique probabilistic measure (online)
  • HotRegion: Predicts hot regions (online)
  • HotPoint: Hotspot Prediction Server For Protein Interfaces (online)
  • FOLDEF: Uses FoldX energies to predict the hot spot residues (online)
  • MutaBind: evaluates the effects of variations and disease mutations on protein-protein interactions only for soluble complexes (online)
  • Piface: A Clustered Protein-Protein Interface Database (online)
  • ProtCID: Protein Common Interfaces Database (online)
  • Patch-DCA: Improved Protein Interface Prediction by utilizing Structural Information and Clustering DCA scores (standalone)
  • PAIRPred: Partner Aware Interacting Residue PREDictor (standalone)
  • PPISP: Protein-protein interaction site prediction through combining local and global features with deep neural networks (online and standalone)
  • SCRIBER: accurate and partner type-specific prediction of protein-binding residues from proteins sequences (online)
  • IDRBind: protein interface predictor for binding sites of intrinsically disordered protein regions (IDRs), ranging from peptide motifs (i.e., short linear motifs) to molecular recognition features (MoRFs) (online)
  • PRODIGY-crystal: classification of biological interfaces in protein complexes (online)
  • SeRenDIP: SEquential REmasteriNg to DerIve Profiles for fast and accurate predictions of PPI interface positions, sequence-based (online, standalone and datasets)
  • PIZSA: an empirical scoring scheme for evaluation of protein-protein interactions (online)
  • 3DPatch: fast 3D structure visualization with residue conservation (online)
  • MoRFpred: Predicting Functions of Disordered Proteins, input sequence (online)
  • BIPSPI: a method for the prediction of Partner-Specific Protein-Protein Interfaces. BIPSPI employs Extreme Gradient Boosting (XGBoost) models trained on the residue pairs of the protein complexes, input sequences or PDB (online)
  • ArDock: Identification and visualization of protein binding regions. Arbitrary docking can reveal potential interaction sites on the surface of a protein using docking with a set of 25 random protein probes (online)
  • ComplexContact: inter-protein contact prediction using deep learning (RaptorX-contact, input sequences, online)
  • DIBS: a repository of disordered binding sites mediating interactions with ordered proteins - database (online)
  • iPred scans the surface of a protein structure and identifies potential hotspots, input PDB (online)
  • IChemPIC Random forest classifier of biological and crystallographic protein-protein interfaces, input PDB (online)
  • SpotOn: Identification of Protein-Protein Interface Hot-Spots, requires PDB as input (online)
  • metaPPI: meta approach to predict protein-protein interaction binding site, input PDB (online)
  • meta-PPISP: a meta web server for protein-protein interaction site prediction (online)
  • PresCont: tools to predict interface residues input PDB, seq alignment, many other tools to predict structurally important residues (CLIPS-1D), residues important for protein function (H2r), generation of consensus seq logo (cSeqLogo) online
  • Cons-PPISP: consensus neural network method for predicting protein-protein interaction sites, input PDB (online)
  • bindML:Predicting Protein-Protein Interaction Sites using Phylogenetic Substitution Models, input PDB and sequence alignment (online)
  • SPIDDER: Solvent accessibility based Protein-Protein Interface iDEntification and Recognition, input PDB, could also be sequences (online)
  • Patch Finder: the new version is called BindUP (BindUP: a web server for non-homology-based prediction of DNA and RNA binding proteins, including all PatchFinderPlus features), input PDB (online)
  • DNAproDB: web-based database and structural analysis tool that offers a combination of data visualization, data processing and search functionality that improves the speed and ease with which researchers can analyze, access and visualize structural data of DNA-protein complexes (online)
  • InterProSurf: predict functionally important amino acids on protein surface crucial for protein function and protein-protein interaction (many other tools, GetArea, EpiSearch to predict conformational epitopes...) online
  • Pred_PPI: Based on auto covariance (AC) and support vector machine (SVM), this tool is capable of predicting PPIs for any target protein pair only using their primary sequences (online)
  • PredUs: uses structural information to predict what residues on protein surfaces are likely to participate in complexes with other proteins, input PDB (online)
  • iFraG: a protein-protein binding site prediction server based on common minimal sequence fragments with known interacting protein pairs, input sequences (online)
  • PSC: Protein Surface Classification by the spatial patterns of functional surfaces: insights into the binding sites, molecular functions and structural evolution (online)
  • The database JET2 Viewer (putative protein binding sites, PPI, pocket descriptors, for all PDB structures) (online)
  • ProteinPlus: Visualize structures and create 2D pose depictions, prepare proteins for docking, add hydrogens (Protoss), predict binding pockets (DoGSiteScorer), visualize electron density (EDIA), Screening of structures based on selection criteria (StructureProfiler), Find structural data of the PDB to activity values stored in the ChEMBL database (ActivityFinder), add water molecules...input PDB (online)
  • StructureProfiler: an all-in-one tool for 3D protein structure profiling - prepare datasets (online via ProteinPlus and standalone)
  • IBIS (Inferred Biomolecular Interaction Server)
  • PISA (PDBePISA, interactive tool for the exploration of macromolecular interfaces, input PDB, online)
  • EPPIC: Evolutionary Protein-Protein Interface Classifier...input PDB (online)

Protein-protein complex prediction - template-based

  • Struct2Net: makes structure-based computational predictions of protein-protein interactions (online)
  • iWrap: novel threading based protein-protein interaction prediction program (standalone)
  • INstruct: a database of 3D protein interactome networks with structural resolution (online)
  • COTH: a multiple-chain protein threading algorithm which is designed to identify and recombine protein complex structures from both tertiary and complex structure libraries (online)
  • HOMCOS: Searching and Modeling of 3D Structures of Complexes (online)
  • Interactome3D: web service for the structural annotation of protein-protein interaction networks. Submit your interactions and the server will find all the available structural data for both the single interactors and the interactions themselves (online)
  • PrePPI: a database of predicted and experimentally determined protein-protein interactions (PPI) for the human proteome (online)
  • iLoops: predict interactions (online
  • SPRING: template-base algorithm for protein-protein complex structure prediction (online)

Protein-membrane (transient or not) + interaction

  • PMIpred: Protein-Membrane Interaction predictor (online), 2024.
  • MODA: membrane optimal docking area, find membrane binding sites on a protein (online)
  • MPA-Pred: A machine learning approach for predicting the binding affinity of membrane protein-protein complexes (online)
  • DREAMM: server for drugging protein-membrane interfaces as a novel workflow for targeted drug design (online)
  • ReSMAP: Predict Residue-Specific Membrane-Association Propensities of Intrinsically Disordered Proteins (online)
  • PyLipID: A Python Package For Lipid Interactions Analysis (standalone)
  • PPM 3.0: Spatial arrangement of proteins in planar and curved membranes (online)
  • ATOLL: Comparing transmembrane protein structures (online and standalone)
  • PPIMem: a novel approach for predicting transmembrane protein-protein complexes (online database)
  • PoreLogo: Visualization of sequence and conservation of pore-lining residues in transmembrane protein structures (online)
  • TMDOCK Server: predicts formation of dimeric complexes by single-spanning transmembrane (TM) proteins (online)
  • PoreWalker: Detection and characterisation of transmembrane protein channels (online)
  • TMPfold: A Web Tool for Predicting Stability of Transmembrane Helix Association (online)
  • PerMM: Tool and Database for Analysis of Passive Membrane Permeability and Translocation Pathways of Bioactive Molecules (online)
  • MERMAID: web server to prepare and run coarse-grained membrane protein dynamics (online)
  • CGMD Platform: Integrated Web Servers for the Preparation, Running, and Analysis of Coarse-Grained Molecular Dynamics Simulations (online)
  • PredMP: a web server for de novo prediction and visualization of membrane proteins (online)
  • MemBrain: An Easy-to-Use Online Webserver for Transmembrane Protein Structure Prediction (online)
  • PureseqTM: efficient and accurate prediction of transmembrane topology from amino acid sequence only (online)
  • MENSAdb: a thorough structural analysis of membrane protein dimers (online)
  • FMAP 2.0: Thermodynamics-Based Molecular Modeling of Helices in Membranes and Micelles (online)
  • EncoMPASS: Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry (online)
  • LipidBuilder: and micelle generator (online)
  • ANVIL (Assignment aNd VIsualization of the Lipid bilayer) (standalone)
  • Micelle Maker: online
  • PPM server: calculates rotational and translational positions of transmembrane and peripheral proteins in membranes using their 3D structure (PDB coordinate file) as input (online)
  • PerMemDB: A database for eukaryotic peripheral membrane proteins (online)
  • PACKMOL: creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space (standalone)
  • INSert membrANE (INSANE) - coarse grain Martini (standalone)
  • MemBuilder: standalone
  • (Pro)tein (B)ilayer (L)ipid (M)embrane (ProBLM)
  • MemProtMD (Membrane-embedded structures), database of around 3500 intrinsic membrane protein structures (online)
  • RHYTHM A Knowledge Based Prediction of Helix-Helix Contacts (online)
  • CCTOP: a Consensus Constrained (transmembrane) TOPology prediction web server (online)
  • FATSLiM: to analyze MD simulations of membranes (standalone)
  • OPM-DB (prepare protein-membrane systems) online
  • Transmembrane protein Models Positioned in the Lipid bilayer (TMPL, online)
  • Protter (interactive protein feature visualization, online)
  • Memdock (alpha-helical membrane protein docking algorithm, online)
  • TOPCONS: Consensus prediction of membrane protein topology and signal peptides (online)
  • DGpred: deltaG prediction for TM helix insertion (online)
  • Membrane Protein Explorer (MPEx: a tool for exploring the topology and other features of membrane proteins by means of hydropathy plots based upon thermodynamic and biological principles (standalone)
  • CELLmicrocosmos MembraneEditor: online and standalone

Molecular simulation - refinement - flexibility (macromolecules)

  • HydraProt: Deep Learning Tool for Fast and Accurate Prediction of Water Molecule Positions for Protein Structures (standalone, 2024).
  • GlycoSHIELD-MD: simple MD pipeline to generate realistic glycoprotein models (online, 2024).
  • GlycoSHIELD-MD: simple MD pipeline to generate realistic glycoprotein models (standalone, 2024).
  • PART: PART is a command line tool to prevent aggregation between specified residues in a molecular dynamics (MD) simulation. Preventing such aggregation is especially of interest in cosolvent MD simulations with hydrophobic probes. PART will build a PLUMED file based on a strucure file provided by the user. Published in 2024. (online).
  • WEBGRO: MD simulation online with GROMACS (online)
  • Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS (online)
  • 3DDPDs: describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors (standalone - august 2023)
  • AlloReverse: multiscale understanding among hierarchical allosteric regulations (online URL1)
  • AlloReverse: multiscale understanding among hierarchical allosteric regulations (online URL2)
  • Psntools: Python package for protein structure network analysis (standalone)
  • MDiGest: Python package for describing allostery from molecular dynamics simulations (standalone)
  • Springcraft: Biotite extension package that allows the analysis of AtomArray objects via Elastic Network Models (ENMs)(standalone)
  • PyL3dMD: Python LAMMPS 3D molecular descriptors package (standalone)
  • EnGens: a computational framework for generation andanalysis of representative protein conformationalensembles (online)
  • DynaSig-ML: automated learning of biomolecular dynamics–function relationships (standalone)
  • MDSubSampler: a posteriori sampling of important protein conformations from biomolecular simulations (standalone)
  • Uni-GBSA: open-source and web-based automatic workflow to perform MM/GB(PB)SA calculations for virtual screening (online)
  • Uni-GBSA: open-source and web-based automatic workflow to perform MM/GB(PB)SA calculations for virtual screening (standalone)
  • ACPYPE: small molecule MD topology generation (online)
  • ACPYPE: small molecule MD topology generation (standalone)
  • PACKMAN-Molecule: Python toolbox for PACKing and Motion ANalysis (standalone)
  • Compliance: Structural compliance: A new metric for protein flexibility (PACKMAN) (standalone)
  • WaterKit: Thermodynamic Profiling of Protein Hydration Sites (predict water binding sites) (standalone)
  • gmx_qk: An Automated Protein/Protein–Ligand Complex Simulation Workflow Bridged to MM/PBSA, Based on Gromacs and Zenity-Dependent GUI for Beginners in MD Simulation Study (standalone)
  • RING-PyMOL: a set of analysis tools for structural ensembles and molecular dynamic (MD) simulations (residue interaction networks) (standalone)
  • MDBuilder: a PyMOL plugin for the preparation of molecular dynamics simulations (standalone)
  • KIF: Key Interactions Finder, a python package to identify the key molecular interactions that regulate any conformational change (standalone)
  • KOSMOS: normal mode analysis (NMA) based on an elastic network model (ENM) (harmonic and anharmonic analyses) (online)
  • PyContact: a GUI-based tool for rapid, versatile and customizable analysis of non-covalent interactions in molecular dynamics (MD) trajectories (standalone)
  • BioBB-Wfs: BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations (online)
  • MDTraj: investigate MD data and compute buried SASA… (standalone)
  • ColabFold: making protein folding accessible to all (standalone)
  • YAMACS: graphical user interface for the GROMACS program (standalone)
  • DeepDriveMD: Deep-Learning Driven Adaptive Molecular Simulations (standalone)
  • pyFoldX: enabling biomolecular analysis and engineering along structural ensembles (standalone)
  • ExProSE: Predicting Protein Dynamics and Allostery Using Multi-Protein Atomic Distance Constraints (standalone)
  • DCI: Coarse-Grained Protein Structures into Their Dynamic Communities with DCI, A Dynamic Community Identifier (online)
  • HOPMA: Boosting Protein Functional Dynamics with Colored Contact Maps (standalone)
  • PSNtools: PSNtools for standalone and web-based structure network analyses of conformational ensembles (high throughput investigation of allosterism in biological systems) (online)
  • PDBCor: Extraction of the correlations from the multistate pdb protein coordinates (online)
  • MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics (online and standalone)
  • 3dRS: a Web-Based Tool to Share Interactive Representations of 3D Biomolecular Structures and Molecular Dynamics Trajectories (data sharing) (online)
  • GridSolvate: A Web Server for the Prediction of Biomolecular Hydration Properties (predicts the distribution of hydration sites within proteins) (online)
  • MolADI: A Web Server for Automatic Analysis of Protein-Small Molecule Dynamic Interactions (using a structure and a trajectory as inputs, users can pinpoint whether certain specific interactions exist in a particular frame and keep track their variations along the dynamic trajectory) (online)
  • CLoNe: automated clustering based on local density neighborhoods for application to biomolecular structural ensembles (standalone)
  • NRGTEN Python package: an extensible toolkit for coarse-grained normal mode analysis of proteins, nucleic acids, small molecules and their complexes (standalone)
  • MEDUSA: Multiclass flexibility prediction from sequences of amino acids (online, this is not a simulation tool)
  • SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions (PPI) (online) (or http://sbi.upf.edu/spserver/)
  • CGMD Platform: Integrated Web Servers for the Preparation, Running, and Analysis of Coarse-Grained Molecular Dynamics Simulations (online)
  • SIRAH: Coarse-Grained forcefield for Gromacs and Amber (standalone)
  • PyLAT: Python LAMMPS (molecular dynamics package) Analysis Tools. Enables users to compute viscosities, self-diffusivities, ionic conductivities, molecule or ion pair lifetimes, dielectric constants, and radial distribution functions (standalone)
  • Enlighten2: Protocols and tools to run (automated) atomistic simulations (molecular dynamics) of enzyme-ligand systems (Python, PyMOL plugin, standalone)
  • NAMD: a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. Simulation preparation, energy minimization... and analysis is integrated into the visualization package VMD (standalone)
  • OPUS-Refine: A Fast Sampling-Based Framework for Refining Protein Backbone Torsion Angles and Global Conformation (standalone)
  • ProtoCaller: Robust Automation of Binding Free Energy Calculations.It is a Python library distributed through Anaconda which automates relative protein-ligand binding free energies in GROMACS (standalone)
  • MODE-TASK: large-scale protein motion tools (analysing normal modes and performing principal component analysis) (standalone)
  • AIR: Artificial Intelligence-Based Multi-Objective Optimization Protocol for Protein Structure Refinement (standalone)
  • P3Fold: Fast and Flexible Coarse-grained Prediction of Protein Folding Routes using Ensemble Modelling and Evolutionary Sequence Variation (online)
  • LARMD: integration of bioinformatic resources to profile ligand-driven protein dynamics. Normal mode analysis is also provided. Ligand binding, unbinding… (online)
  • NCIPLOT4: used to investigate noncovalent interactions (NCI) (i.e. hydrogen bonds, steric clashes and van der Waals) in systems ranging from small molecules to large biosystems (standalone)
  • ProDy: free and open-source Python package for protein structural dynamics analysis (standalone)
  • SignDy: Signature Dynamics of Protein Families. Calculates the signature dynamics of families of proteins that share similar folds, but not necessarily similar sequences(standalone)
  • SMOG: Structure-based Models for Biomolecules (online)
  • GOdMD: GO discrete Molecular Dynamics. Conformational Transitions with Coarse-Grained Dynamics (standalone or online)
  • FlexServ: shows in an easy and visual way flexibility-related properties of proteins (online)
  • UNRES: study protein folding by molecular simulations, coarse grain (standalone)
  • UNRES server: ab initio simulations of protein structure and dynamics by using the coarse-grained UNRES model (online)
  • SABBAC: Structural Alphabet based protein Backbone Builder from Alpha Carbon trace (online)
  • LAMMPS: Molecular Dynamics Simulator and much more (standalone, a protocol for Mac is also presented)
  • AWSEM-MD: a coarse-grained protein simulation package (Associative Memory, Water Mediated, Structure and Energy Model) which is implemented as a package for the LAMMPS tool (standalone but web server also available)
  • ProPHet: program combines a coarse-grain and elastic network (ENM) protein model and a Brownian Dynamics algorithm to compute protein local rigidity at the residue level (online)
  • PRS: Perturbation Response Scanning. PRS calculates the effectiveness and sensitivity of residues in propagating allosteric signals (standalone)
  • coMD: hybrid method with a VMD plugin designed for efficient simulations of conformational changes (standalone)
  • BitClust: Fast and memory efficient clustering of long Molecular Dynamics (standalone)
  • ENCoM: coarse-grained normal mode analysis method (can be used to investigate mutations) (standalone)
  • MDAnalysis: a toolkit for the analysis of molecular dynamics simulations (standalone python)
  • MDsrv: viewing and sharing molecular dynamics simulations on the web (online)
  • Tios: The Internet of Simulations. Turning Molecular Dynamics into a Data Streaming Web Application (standalone)
  • KBbox: A Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding (online advices for tool selection)
  • DDT: Drug Discovery Tool, a fast and intuitive graphics user interface for Docking (autodock) and Molecular Dynamics analysis (standalone)
  • GPathFinder: extension built over GaudiMM core to allow the identification of ligand binding pathways at atomistic level (standalone)
  • MERMAID: web server to prepare and run coarse-grained membrane protein dynamics (online)
  • PyRod: Tracing water molecules in molecular dynamics simulations to predict hotspots and binding pockets. Can be used to define pharmacophore models (standalone)
  • SNP2SIM: a modular workflow for standardizing molecular simulation and functional analysis of protein variants (standalone)
  • Kinact: a computational approach for predicting activating missense mutations in protein kinases (online)
  • SAMSON: ligand unbinding pathways (standalone)
  • Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Polarizable Force Fields
  • CABS-flex: a simulation environment for fast modeling of protein flexibility (standalone)
  • gRINN :a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations
  • MODE-TASK Large-scale protein motion tools
  • CABS-flex :fast simulations of flexibility of protein structures
  • Pyrite: A blender plugin for visualizing molecular dynamics simulations using industry-standard rendering techniques
  • Scoria: a Python module for manipulating 3D molecular data
  • HullRad Fast Calculations of Folded and Disordered Protein and Nucleic Acid Hydrodynamic Properties
  • STOCK: The structure mapping tool allows one to map an atomistic representation of a single molecule to a coarse-grained representation. The end result is a topology and weights mapping XML file as is used in VOTCA or DL CGMAP coarse-graining simulation packages (online)
  • DynaMine Fast predictor of protein backbone dynamics using only sequence information as input
  • QwikMD MD with VMD and NAMD (standalone Mac, Linux, Windows, Supercomputers)
  • WEBnm@ Web server and services for comparing protein flexibility
  • NMSim integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins
  • FoldX (simulation, Alascan, mutation, peptides...loops)
  • FoldX 5.0: Working with RNA, small molecules and a new graphical interface (standalone)
  • Naccess: calculates the accessible area of a molecule from a PDB file
  • FreeSASA: calculates the accessible area of molecules, different chains, etc
  • dr_SASA: Calculation of accurate interatomic contact surface areas for the quantitative analysis of non-bonded molecular interactions (online and standalone multiple OS)
  • ProteinPrepare Make your protein ready for molecular dynamics simulations by titrating and protonating the protein at a desired pH and by optimizing the H-bond network
  • Adaptativesampling Explore the protein conformational space or protein-ligand interaction space by running MD simulations along the metric of your choice
  • PREFMD: protein structure refinement via molecular dynamics simulations (Online and Standalone scripts also available)
  • Abalone: Molecular simulations with AMBER-ii force field, Molecular Dynamics folding
  • AQUASOL predict water binding sites
  • DRoP: Automated detection of conserved solvent binding sites on proteins (online with login and standalone)
  • VLDP tool for analysing protein structures based on Laguerre diagram, can also be used to add water online
  • PreFRP: Prediction and visualization of fluctuation residues in protein structure (online)
  • 3Drefine: protein structure refinement server (online)
  • ModRefiner: atomic-level, high-resolution protein structure refinement (online)
  • FG-MD: molecular dynamics (MD) based algorithm for atomic-level protein structure refinement (online)
  • NOMAD-ref: Normal mode calculation and visualisation (online)
  • iMODS: explore the colletive motions of proteins and nucleic acids using NMA in internal coordinates (torsional space) (online)
  • WEBnma: Web-server for Normal Mode Analysis of proteins (online)
  • MDWeb: personal workspace providing standard protocols to prepare structures, run standard molecular dynamics simulations and to analyze trajectories (online)
  • Gromacs: via the WeNMR suite for Structural Biology (online)
  • AMBER: suite of biomolecular simulation programs (standalone)
  • CHARMM: Chemistry at HARvard Macromolecular Mechanics (standalone)
  • CHARMM-GUI (eg solvator to add water molecules...)
  • DynOmics (dynamics of structural proteome) (online)
  • DynOmics: DynOmics Portal for computing and visualizing biomolecular systems dynamics (ENM, iGNM (Gaussian network model), ProDy, Anisotropic network model)(online)
  • ESSA: Essential site scanning analysis: A new approach for detecting sites that modulate the dispersion of protein global motions (Essential sites are defined as residues that would significantly alter the protein’s global dynamics if bound to a ligand) (standalone)
  • SignDy: pipeline composed of seven steps designed to enable and automate the evaluation and comparison of the dynamics of structures belonging to evolutionarily related proteins. SignDy is built upon the Protein Dynamics (ProDy) API (standalone)
  • Amber tools: a suite of biomolecular simulation programs (standalone)
  • SEBOMD: Semi-Empirical Born–Oppenheimer Molecular Dynamics (SEBOMD) within the Amber Biomolecular Package (standalone)
  • YASARA: molecular-graphics, -modeling and -simulation program (standalone)
  • GROMITA-GUI: Graphical User Interface (GUI) front-end for the molecular sumulation package, GROMACS (standalone)
  • Gromacs: molecular simulation (standalone)
  • WnS: Systematic exploration of multiple drug binding sites, Wrap 'n' Shake (WnS) (combine AutoDock 4.2.3 and GROMACS) (standalone)
  • FireProt: automated design of thermostable proteins (online)
  • SEEKR: scripts for ligand-receptor kinetic calculations (standalone)
  • NWChem: High-Performance Computational Chemistry (standalone)
  • MCTBI: metal ion effects in RNA structures (online)
  • SimRNAweb: simulation RNA (online)
  • 3D-NuS: simulation non-canonical 3-Dimensional Nucleic Acid Structures (online)
  • CHARMM-GUI: provides a web-based graphical user interface to generate various molecular simulation systems and input files (online)
  • FlexPred: Protein fluctuation prediction using SVR (online)
  • SPECTRUS: performs a decomposition into quasi-rigid domains of proteins or protein complexes, based on the analysis of the distance fluctuations between pairs of amino acids (online)
  • Bio3D-web NMA: normal mode analysis of protein structures (elastic network models (ENMs), residue fluctuations, mode visualization...(online)
  • LipidBuilder: online
  • HTMD: a molecular-specific programmable environment to prepare, handle, simulate, visualize and analyze molecular systems (standalone)

Electrostatics of macromolecules (mainly and molecular surface properties)

  • DeepKa: deep-learning-based protein pKa predictor (online)
  • PypKa: a flexible Python module for Poisson-Boltzmann based pKa calculations (for proteins) (standalone)
  • patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures (online)
  • SURFMAP: a software for mapping in two dimensions protein surface features (standalone)
  • Graph-pKa: Multi-instance learning of graph neural networks for aqueous pKa prediction (online)
  • DispHScan: A Multi-Sequence Web Tool for Predicting Protein Disorder as a Function of pH (online)
  • Bluues: Electrostatic properties of proteins based on generalized Born radii (online)
  • DFMD: Fast and Effective DelPhiForce Steered Molecular Dynamics Approach to Model Ligand Approach Toward a Receptor (standalone)
  • PROPKA: predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure (standalone Python)
  • PKAD: a database of experimentally measured pKa values of ionizable groups in proteins (online database)
  • APBS and PDB2PQR: electrostatic and solvation properties for complex molecules (online and standalone)
  • ProteinPrepare Make your protein ready for molecular dynamics simulations by titrating and protonating the protein at a desired pH and by optimizing the H-bond network (online)
  • Protein-Sol: Web-based display of protein surface and pH-dependent properties for assessing the developability of biotherapeutics (with 3D data) (online)
  • TKSA-MC: A Web Server for rational mutation through the optimization of protein charge interactions (Tanford-Kirkwood Surface Accessibility model) (standalone on GitHub) (online)
  • PBEQ Solver: calculates and visualizes the electrostatic potential of a molecule by solving the Poisson-Boltzmann (PB) equation (online)
  • PCE: Protein Continuum Electrostatics (electrostatic potentials and pKa) (online)
  • H++: automated system that computes pK values of ionizable groups in macromolecules and adds missing hydrogen atoms according to the specified pH of the environment (online)
  • DelPhiPKa: protonation and pKa calculation (online)
  • DelPhiForce: electrostatic forces and energy calculations and visualization between two objects (online)
  • ESBRI Evaluating the Salt BRIdges in Proteins (online)
  • SMPBS: size Modified Poisson-Boltzmann Solvers (online)
  • PDBparam: check salt-bridges, cation-pi, etc (online)

Ligand-binding pockets

  • ClassyPose: A Machine-Learning Classification Model for Ligand Pose Selection Applied to Virtual Screening in Drug Discovery (standalone, 2024).
  • AHoJ-DB: Given the Holo form of a protein find apo-proteins, find other bound forms..align both apo- and holo-proteins to the query holo protein and given the Apo form of a protein find all other forms... (online, 2024).
  • HydraProt: Deep Learning Tool for Fast and Accurate Prediction of Water Molecule Positions for Protein Structures (standalone, 2024).
  • SiteMine: Large-scale binding site similarity searching in protein structure databases (online), 2024.
  • CRAFT: cavity prediction tool based on flow transfer algorithm (standalone), 2024.
  • CRAFT: cavity prediction tool based on flow transfer algorithm (online), 2024.
  • BindingNet: 69,816 modeled high-quality protein–ligand complex structures with experimental binding affinity data (online)
  • BindingNet: 69,816 modeled high-quality protein–ligand complex structures with experimental binding affinity data (standalone)
  • COLLAPSE: A representation learning framework for identification and characterization of protein structural sites (standalone)
  • AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands (standalone)
  • AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands (online)
  • PDBspheres: a method for finding 3D similarities in local regions in proteins (pocket similarity) (standalone)
  • IF-SitePred: method for predicting ligand-binding sites on protein structures (2023) (standalone)
  • PUResNet: Predicting protein-ligand binding sites using deep convolutional neural network (binding pocket) (standalone)
  • PASSerRank: Prediction of allosteric sites with learning to rank (online)
  • PASSerRank: Prediction of allosteric sites with learning to rank (standalone)
  • pyCaverDock: Python Implementation of the Popular Tool for Analysis of Ligand Transport with Advanced Caching and Batch Calculation Support (standalone)
  • BiteNet: Spatiotemporal identification of druggable binding sites using deep learning (standalone)
  • PDBspheres: a method for finding 3D similarities in local regions in proteins (standalone)
  • PocketMiner: predicting the locations of cryptic pockets from single protein structures (online)
  • PocketMiner: predicting the locations of cryptic pockets from single protein structures (standalone)
  • AI-Bind: Improving the generalizability of protein-ligand binding predictions with AI-Bind (standalone)
  • SubPEx: Sub-Pocket EXplorer, a weighted-ensemble method to enhance binding-pocket conformational sampling (online & standalone)
  • SubPEx: Sub-Pocket EXplorer, a weighted-ensemble method to enhance binding-pocket conformational sampling (online & standalone)
  • KVFinder-web: application for detecting and characterizing biomolecular cavities (online)
  • PASSer: fast and accurate prediction of protein allosteric sites (online)
  • Allopath: allosteric pathways with network analysis (standalone)
  • APOP: Predicting Allosteric Pockets in Protein Biological Assemblages (standalone)
  • APOP: Predicting Allosteric Pockets in Protein Biological Assemblages (online)
  • Pocket to Concavity (P2C): tool for refining the of Protein-Ligand binding site shape from alpha-spheres (standalone)
  • Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets (generative chemistry) (standalone)
  • LigBind: identifying binding residues for over 1000 ligands with relation-aware graph neural networks (functional binding residues prediction) (online)
  • LigBind: identifying binding residues for over 1000 ligands with relation-aware graph neural networks (functional binding residues prediction) (standalone)
  • ACP4: 3D-Sensitive Encoding of Pharmacophore Features (compare ligand in 3D or ligand-binding sites (holo structures) can compare pockets) (standalone)
  • ROSIE: Rosetta Online Server that Includes Everyone many tools includinc Make_Exemplar Protocol to investigate binding pocket (online)
  • AlphaSpace2: surface topographical mapping tool (investigate and analyze pockets, pocket comparison and much more ) (standalone)
  • PyVOL: python library packaged into a PyMOL GUI for identifying protein binding pockets, find volume, also via python command line (standalone)
  • ProteinPocketDetection: Protein pocket detection via convex hull surface evolution and associated Reeb graph (standalone)
  • ProteinPocketDetection: Protein pocket detection via convex hull surface evolution and associated Reeb graph (online)
  • PointSite: a point cloud segmentation tool for identification of protein ligand binding atoms (standalone)
  • MoloVol: free, cross-plattform, scientific software for volume and surface computations of single molecules and crystallographic unit cells (standalone)
  • PocketDruggability: A model that predicts the “attainable binding affinity” for a given binding pocket on a protein; this model relies on 13 physiochemical and structural features calculated using the protein structure (standalone)
  • PocketOptimizer 2.0: Design of small molecule‐binding pockets in proteins (standalone)
  • pyKVFinder: Python package for biomolecular cavity detection and characterization in data science (standalone)
  • PocketAnalyzerPCA: Identify cavities and crevices in proteins (standalone)
  • Panther: A novel tool to predict small molecule binding into proteins (python, standalone)
  • Chanalyzer: a computational geometry approach for the analysis of protein channel shape and dynamics (standalone)
  • SiteFerret: beyond simple pocket identification in proteins (standalone)
  • CavBench: A benchmark for protein cavity detection methods (standalone)
  • FrustraPocket: A protein–ligand binding site predictor using energetic local frustration (standalone)
  • CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning (PPI and regular binding sites) (online)
  • GRaSP-py: a graph-based residue neighborhood strategy to predict binding sites (standalone)
  • AlphaSpace2: fragment-centric topographical mapping (eg., to target PPIs, binding site detection, comparison, and design) (standalone)
  • FastGrow: a fast fragment growing approach using a shape-based algorithm. It also features pharmacophore-like constraints, geometry optimization, and built-in ensemble flexibility (online)
  • ProBiS-Fold: Annotation of Human Structures from the AlphaFold Database with No Corresponding Structure in the PDB to Discover New Druggable Binding Sites (online database)
  • HProteome-BSite: a database for ligand binding sites in human proteome (online)
  • PathDetect-SOM: A Neural Network Approach for the Identification of Pathways in Ligand Binding Simulations (standalone)
  • DREAMM: server for drugging protein-membrane interfaces as a novel workflow for targeted drug design (online)
  • BindWeb: a web server for ligand binding residue and pocket prediction from protein structures (online)
  • Graphsite-classifier: deep graph neural network to classify ligand-binding sites on proteins (standalone)
  • Allo: a tool for dicriminating and prioritizing allosteric pockets (standalone)
  • AlloDriver: utilizes structural and dynamic features to prioritize potentially functional genes/proteins in individual cancer via mapping gene mutations generated from cancer samples to allosteric/orthosteric sites derived from protein three-dimensional structures (online)
  • MCPath: Monte Carlo (MC) path generation approach to predict likely allosteric pathways and functional residues (online)
  • AllosMod: Modeling of Ligand-induced Protein Dynamics and Beyond (allostery) (online)
  • Caviar: Protein cavity identification and automatic subpocket decomposition (standalone)
  • CROMATIC: Cross-Relationship Map of Cavities from Coronaviruses (Covid-19) (dataset)
  • ExProSE: Predicting Protein Dynamics and Allostery Using Multi-Protein Atomic Distance Constraints (standalone)
  • Mebipred: identifying metal binding potential in protein sequence (web server and standalone) (online)
  • PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures (standalone)
  • PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures (online)
  • PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures (standalone)
  • Kalasanty: Improving detection of protein-ligand binding sites with 3D segmentation (standalone)
  • GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs (online)
  • HoTS: Sequence-based prediction of binding regions and drug-target interactions (standalone)
  • CavitySpace: A database of potential ligand binding sites in the human proteome (alphafold structures) (database)
  • DeepBindPoc: deep learning based method for identifying highly potential pocket for given ligand from a fpocket generated pocket decoys set of the given protein (online)
  • PSnpBind: a database of mutated binding site protein–ligand complexes constructed using a multithreaded virtual screening workflow (online and standalone)
  • TransportTools: biomolecules and ligand transport through them. TransportTools is implemented in Python3 and distributed as pip and conda packages (allostery, cavity...) (standalone)
  • DeeplyTough: compare protein binding pockets (standalone)
  • Ohm: To map allosteric communications, the tool uses percolation theory to identify connections throughout a protein and search for paths between any of its two sites (percolation-inspired pathways mapping and visualization) (online)
  • kissim: a novel fingerprinting strategy designed specifically for kinase pockets, allowing for similarity studies across the structurally covered kinome (standalone)
  • ProteinLens: constructs a fully atomistic, energy-weighted graph representation of a biomolecular structure and explores the long-range communication or connectivity between any specific sites in the system (identify potential allosteric sites, explore allosteric pathways, identify residues that play a key role in signalling and/or cooperativity) (online)
  • MolADI: A Web Server for Automatic Analysis of Protein-Small Molecule Dynamic Interactions (using a structure and a trajectory as inputs, users can pinpoint whether certain specific interactions exist in a particular frame and keep track their variations along the dynamic trajectory) (online)
  • LiBiSCo: Ligand Binding Site Comparison, a tool for analyzing interactions between proteins and ligands to explore amino acid specificity within active sites (the comparison is performed at the ligand atom level irrespectively of having binding site similarity or not between the protein structures of interest) (standalone)
  • DeepPocket: Ligand Binding Site Detection and Segmentation using 3D Convolutional Neural Networks (standalone)
  • DeepSurf: a surface-based deep learning approach for the prediction of ligand binding sites on proteins (standalone)
  • OctSurf: Efficient hierarchical voxel-based molecular surface representation for protein-ligand affinity prediction (standalone)
  • INDEEP: 3D fully convolutional neural networks to assist in silico drug design on protein-protein interactions (standalone)
  • CHARMM-GUI LBS Finder & Refiner: Ligand Binding Site Prediction and Refinement (standalone)
  • ProBiS-Dock Database: A Web Server and Interactive Web Repository of Small Ligand–Protein Binding Sites for Drug Design (online)
  • SpotXplorer: Exploring protein hotspots by optimized fragment pharmacophores (small fragment dataset)
  • TACTICS: machine-learning algorithm (trajectory-based analysis of conformations to identify cryptic sites), which uses an ensemble of molecular structures (such as molecular dynamics simulation data) as input (standalone)
  • BiteNet: large-scale detection of protein binding sites (online)
  • Site2Vec: a reference frame invariant algorithm for vector embedding of 3D protein–ligand binding sites (online)
  • SARSCoV2_pocketome: Genetic variability of SARS-CoV-2 drug binding sites, COVID-19 (online)
  • FRAGSITE2: A Structure and Fragment Based Approach for Virtual Ligand Screening (online)
  • FRAGSITE: A Fragment-Based Approach for Virtual Ligand Screening. For virtual ligand screening: screening a protein against library of compounds. For virtual target screening: screening a compound against the Human proteome (online)
  • ACCLUSTER: predicts peptide binding sites on a given protein structure by clustering chemical interactions between amino acid probes and the protein receptor (online)
  • GeoMine: Interactive Pattern Mining of Protein-Ligand Interfaces in the Protein Data Bank (online)
  • CPIPE: investigates reactivity and predicts possible functional roles of protein Cysteine residues. Covalent drug ideas (online)
  • CPIPE: investigates reactivity and predicts possible functional roles of protein Cysteine residues (online)
  • Cysteine binder collection: Cysteine Focused Covalent Inhibitor Library (dataset, commercial)
  • CovPDB: a high-resolution coverage of the covalent protein–ligand interactome (online database)
  • DeepCys: structure-based multiple cysteine function prediction method trained on deep neural network (online and standalone)
  • GraphBind: Functional binding residues prediction (e.g., nucleic-acid-binding residues) (online)
  • HKPocket: human kinase pocket database for drug design (online)
  • MolAICal: tools for 3D drug design of protein targets by artificial intelligence and classical algorithm (de novo design in protein pockets, fragment-based...) (standalone)
  • ECONTACT: Energetic contributions of amino acid residues and its cross‐talk to delineate ligand‐binding mechanism. The ECONTACT approach transforms the per-residue energy terms derived from multiple protein-ligand complexes into orthogonal space using PCA to identify the most variable amino acid residues involved in cross-talk to promote ligand binding (standalone)
  • Erebus: Protein rigid substructure search (online, requires login)
  • ProCare: A Point Cloud Registration Approach to Align Protein Cavities (standalone)
  • Fragment Hotspot Maps: Identifying the interactions that determine fragment binding at protein hotspots (online)
  • Hotspots API: A Python Package for the Detection of Small Molecule Binding Hotspots and Application to Structure-Based Drug Design (fragment mapping) (standalone)
  • visGReMLIN: Graph Mining-Based Detection and Visualization of Conserved Motifs at 3D Protein-Ligand Interface at the Atomic Level (online)
  • Kinase Exosite: Druggable Exosites of the Human Kino-Pocketome (online)
  • D3Pockets: A Method and Web Server for Systematic Analysis of Protein Pocket Dynamics (online)
  • DELIA: Protein-ligand Binding Residue Prediction Enhancement Through Hybrid Deep Heterogeneous Learning of Sequence and Structure Data (online)
  • BionoiNet: Ligand-binding Site Classification With Off-The-Shelf Deep Neural Network (nucleotide- and heme-binding sites) (standalone)
  • LARMD: integration of bioinformatic resources to profile ligand-driven protein dynamics. Normal mode analysis is also provided. Ligand binding, unbinding… (online)
  • eModel-BDB: database of comparative structure models of drug-target interactions from the Binding Database (database online)
  • IsoMIF: identifies binding site molecular interaction field similarities between proteins (standalone)
  • GetCleft: The detection of cavities, both internal or surface-exposed (standalone)
  • PocketPipe: A computational pipeline for integrated Pocketome prediction and comparison (predict with P2RANK and compare with PocketMatch) (standalone)
  • PPIome: Exhaustive Repertoire of Druggable Cavities at Protein-Protein Interfaces of Known Three-Dimensional Structure (online)
  • GPathFinder: extension built over GaudiMM core to allow the identification of ligand binding pathways at atomistic level (standalone)
  • CB-Dock2: a web server for cavity detection-guided protein-ligand blind docking (online)
  • LPIcom: web server developed for understanding protein-ligand interaction for almost all ligands available in Protein Data Bank (online)
  • DRoP: Automated detection of conserved solvent binding sites on proteins (online with login and standalone)
  • PatchSearch: a web server for off-target protein identification (input a protein complexed with a ligand and identifies within user-defined or predefined collections of protein structures, those having a binding site compatible with this ligand in terms of geometry and physicochemical properties) (online)
  • Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport (built on top Caver 3.02 and CaverDock 1.0) (online)
  • PrankWeb: a web server for ligand binding site prediction and visualization. Users can utilize the server API directly, bypassing the need for a web-based frontend or installation of the P2Rank application (online)
  • Drug ReposER: web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning (pocket comparison, ligand transposition) (online)
  • DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network (standalone)
  • CASBench: A Benchmarking Set of Proteins with Annotated Catalytic and Allosteric Sites in Their Structures (online database test pocket tools or docking)
  • ASBench: benchmarking sets for allosteric discovery (online)
  • PyRod: Tracing water molecules in molecular dynamics simulations to predict hotspots and binding pockets (standalone)
  • ProSPECCTs: A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets
  • PPD: Protein pocket detection via convex hull surface evolution and associated Reeb graph (online & standalone in C)
  • PYWINDOW: Python package for the analysis of structural properties of molecular pores (standalone)
  • P2RANK: novel machine learning-based method for prediction of ligand binding sites from protein structure. P2RANK uses Random Forests classifier to infer ligandability of local chemical neighborhoods near the protein surface which are represented by specific near-surface points and described by aggregating physico-chemical features projected on those points from neighboring protein atoms (standalone)
  • ezCADD: a Rapid 2D/3D Visualization Enabled Web Modeling Environment for Democratizing Computer-Aided Drug Design (small molecule docking, protein docking, 2D/3D interaction viz, de novo lead optimization, pocket search and polypharmacology) online
  • 3DLigandSite : CNIO, predict binding pocket with or without 3D structure of the target (predict binding site and ligand transfer) (online)
  • COACH-D :improved protein–ligand binding sites prediction with refined ligand-binding poses through molecular docking (online)
  • CASTp 3.0 :computed atlas of surface topography of proteins (output can be investigated via Chimera or Pymol) (online)
  • CAVER Analyst 2.0 (Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories (standalone Windows))
  • CavityPlus : Predict CavPharmer (receptor-based pharmacophore modelling), CorrSite2.0 (allosteric ligand-binding sites), and CovCys (druggable cysteine residues) (online)
  • AlloFinder :a strategy for allosteric modulator discovery and allosterome analyses (not for pocket but ligand) (online)
  • BINANA: (BINding ANAlyzer) python tool for analyzing ligand-target interactions (Hbonds, cation-Pi, etc, standalone for linux boxes, may work on Mac), if URL not working, seems to be at GitHub
  • Cryptoscout Predict cryptic sites and druggable cavities on a protein structure using mixed-solvent molecular dynamics simulations in presence of benzene (online)
  • APoc: large-scale identification of similar protein pockets (standalone)
  • PESDserv: Allows high-throughput protein binding site comparison (online)
  • SiteEngine: Predicts regions that can potentially function as binding sites (recognition of geometrical and physico-chemical environments that are similar to known binding sites) (online and standalone)
  • metaPocket 2: meta-method, Fpocket, GHECOM, ConCavity and POCASA (online)
  • EDTSurf: (pocket, surface, pocket depth...) (standalone)
  • The database JET2 Viewer: (putative protein binding sites, PPI, pocket descriptors, for all PDB structures) (online)
  • MoMA-LigPath: Molecular Motion Algorithms (MoMA). Starting from the model of a protein-ligand complex, MoMA-LigPath computes the ligand exit path from the active site to the protein surface using robotics-inspired algorithms (explore tunnels) (online, requires login)
  • BSpred: a neural network based algorithm for predicting binding site of proteins from amino acid sequences (online)
  • ASCONA: a fully automated command line tool for generating sequence alignments and superpositions of protein binding sites (standalone)
  • ISMBLab-Lig: predict binding sites for various types of ligands including ions. Tolerates 3D uncertainties (online)
  • COACH: meta-method (COFACTOR, FINDSITE and ConCavity...) (online)
  • TRAPP : a tool for analysis of transient binding pockets in proteins (online)
  • DrugEBIlity: search for pockets with as input a protein, or a ligand...provides druggability scores (online)
  • AlloSite: allosteric site (online)
  • Screen2: geometry-based (online)
  • SiteHound-web: energy-based (send chemical probes) (online)
  • SiteComp: pocket comparison (online)
  • SiMMap: Provides the graphic visualization of the site-moiety map and anchors elements, including a binding pocket with interacting residues, requires ligand (online)
  • ConCavity: prediction from protein sequence and structure (geometry-based) (online)
  • SplitPocket: geometry-based (online)
  • Pepsite2: Prediction of peptide binding sites on protein surfaces (online)
  • POCASA: geometry-based, pockets and cavities, volume... (online)
  • MolAxis: accurate Identification of Channels in Macromolecules (online)
  • MultiBind Multiple Alignment of Protein Binding Sites: pocket comparison (online)
  • SiteEngines: Functional Sites Structural Search Engine (online)
  • 3D-SURFER (pocket comparison online)
  • G-LoSA: Graph-based Local Structure Alignment - Pocket alignment (standalone)
  • GalaxyWeb: predict binding site (online)
  • FTMAP: energy-based (online requires login)
  • PocketAnnotate (align pockets, comparison) (online)
  • ProBiS-ligands: can transposes ligands to the query protein, pocket comparison (online)
  • DoGSiteScorer: druggability score (online)
  • PocketQuery: energy-based (online)
  • fpocket: mainly geometry-based (standalone)
  • Hpocket: (online)
  • MDpocket: (online)
  • Nucleos: identification of nucleotide-binding sites (online)
  • ACTIVE SITE PREDICTION: compute cavities (online)
  • GHECOM (geometry-based): finding multi-scale pockets on protein surfaces using mathematical morphology (online)
  • Patchsurfer (pocket comparison online)
  • Patch-Surfer 2 (predicts binding ligands, pocket comparison online)
  • SPACER: Predicting Allosteric site (online)
  • iDrug: (online)
  • pocketZebra: Selection and Classification of Subfamily-Specific Binding Sites by Bioinformatic Analysis Of Diverse Protein Families (online)
  • Rbpmap: a web server for mapping binding sites of RNA-binding proteins (online)
  • BMF: Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins (online and standalone)
  • ProBiS: align pocket (online)
  • ProbisLigands (Predict Ligands by Similarity in Binding Sites - online)
  • FunFOLD: binding site from sequence (online)
  • IBIS: IBIS reports protein-protein, protein-small molecule, protein nucleic acids and protein-ion interactions observed in experimentally-determined structural biological assemblies (online)
  • PocketDepth: geometry-based (online)
  • DEPTH (online)
  • LigDig (online)
  • PockDrug: predict on holo and apo (online)
  • AlloPred: allosteric site (online)
  • ProBiS-CHARMMing: (online)
  • CryptoSite: flexibility, Cryptic Binding Sites (online)
  • DrugMiner: potential druggable proteins from sequence (online)
  • canSAR: (online)
  • PLIC: Clusters of similar binding sites in the PDB and analysis of various type of interactions within the clusters (online and standalone)
  • PoSSuM (pocket comparison online)
  • CatSId (pocket comparison online)
  • COFACTOR (pocket comparison online)
  • eF-seek (pocket comparison online)
  • Evolutionary Trace Annotation (ETA) (pocket comparison online)
  • fPOP (pocket comparison online)
  • Imaaagine (pocket comparison online)
  • LabelHash (pocket comparison online)
  • PDBSITE / PDBsitescan (pocket comparison online)
  • pevoSOAR (pocket comparison online)
  • PINTS (pocket comparison online)
  • PocketMatch (pocket comparison online)
  • SeSAW (pocket comparison online)
  • SPRITE (pocket comparison online)
  • SuMo (pocket comparison online)
  • TM-align (pocket comparison online)
  • HOMCOS (analyze interactions) (online)
  • ProteinPlus (structural analysis pockets...): (online)
  • ProteinTools: a toolkit to analyze protein structures (salt-bridge, contact…) (online)
  • IonCom (ion & small ligands) (online)
  • PARS (allosteric pockets) (online)
  • DruGUI: Druggability Analysis (standalone for VMD)
  • Geomfinder (pocket comparison): (online)
  • AutoSite: (standalone)
  • VLDPws (analyze surface & solvate - water) (online)
  • PROPORES (Novel toolkit for identifying pockets, cavities and channels of protein structures) (standalone)
  • EPOS_BP BALLPass (standalone)
  • mutLBSgeneDB mutated binding pockets, database (online)
  • PatchSearch (compare pockets) (standalone)
  • WaterDock-2.0 (PyMol) (standalone)
  • WaterDock-2.0 (standalone)
  • WATsite2.0 (water Pymol plugin)
  • PLImap (fragment mapping) (standalone Astex)
  • LIBRAWA: binding site (online)
  • LIBRA+: binding site (standalone)
  • DeepSite (binding pocket predictor, neural networks) (online)
  • IBIS (Inferred Biomolecular Interaction Server) (online)
  • omiXcore: prediction of protein-RNA interactions (online)
  • IChem (Toolkit for detecting, comparing and predicting protein-ligand interactions) (standalone)
  • STarMir (miRNA binding sites on a target mRNA) (online)
  • ChannelsDB : database for the positions, geometry and physicochemical properties of channels (pores and tunnels) found within biomacromolecular structures (eg, in CYP or membrane proteins...) (online)
  • LigQ: a Webserver to Select and Prepare Ligands for Virtual Screening (online)

Biostructural pathology / Structural analysis

Amino acid changes in the 3D structures can be introduced with PyMOL, Chimera, or online with PDB_HYDRO, used for adding water, to mutate...

Variation - mutation databases

  • Missense3D-TM: Predicting the Effect of Missense Variants in Helical Transmembrane Protein Regions Using 3D Protein Structures (online)
  • AlloMAPS 2: allosteric fingerprints of the AlphaFold and Pfam-trRosetta predicted structures for engineering and design (Allosteric Mutation Analysis and Polymorphism of Signalling) (online)
  • Alphamissense: Accurate proteome-wide missense variant effect prediction with AlphaMissense (standalone)
  • COSMIC, COSMIC-3D...: Catalogue Of Somatic Mutations In Cancer
  • Animal-SNPAtlas: a comprehensive SNP database for multiple animals database (online)
  • VARAdb: non-coding variants (online)
  • CoV-GLUE: a database of amino acid replacements, insertions and deletions which have been observed in GISAID hCoV-19 sequences sampled from the pandemic (online)
  • MGI: Mouse Genome Informatics, Human - Mouse: Disease Connection, Vertebrate Homology (mouse, human, rat,and zebrafish), Gene expression (online database)
  • Protabank: A Modern Protein Engineering Database. Explore the Impact of Protein Mutations (online)
  • ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years (online)
  • FireProtDB: database of manually curated protein stability data (online)
  • ThermoMutDB: a thermodynamic database for missense mutations (online)
  • CAUSALdb: A database for disease/trait causal variants identified using summary statistics of genome-wide association studies (online)
  • CircosVCF: circos visualization of whole-genome sequence variations stored in VCF files - circular dataviz (online)
  • i-COMS: A webserver to calculate correlated mutations between proteins (online)
  • SwissVar: portal to search variants in Swiss-Prot entries of the UniProt Knowledgebase (UniProtKB) (online)
  • dbDSM: a manually curated database for deleterious synonymous mutations (single nucleotide mutation which replaces one base to another in the coding sequence that does not alter amino acids in the translated protein due to the degeneracy genetic code, affecting transcript splicing, mRNA stability, RNA secondary structure, the biding site of transcription factor binding and microRNA) (online)
  • CAGI Workshop: Assessing the future of genome interpretation (datasets)
  • GRASP: Genome-wide Repository of Associations between SNPs and Phenotypes (datasets)
  • dbVar: NCBI's database of human genomic structural variation — insertions, deletions, duplications, inversions, mobile elements, translocations, and others (database online)
  • OMIM: Online Mendelian Inheritance in Man (database online)
  • dbSNP: contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations (database online)
  • TCGA: Cancer Genome Atlas (database online)
  • HumDiv/HumVar: Human Disease Variants (database online)
  • The Genome Aggregation Database (gnomAD): aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects (database online)
  • Kaviar: Known VARiants (database online)
  • SKEMPI: Database of binding free energy changes upon mutation (database online)
  • ProNit: Database of thermodynamic data for protein-nucleic acid interactions (database online)
  • ProTherm: Database of thermodynamic data for protein stability (database online)
  • mutLBSgeneDB: Mutated ligand binding site gene DataBase (database online)
  • Platinum: Database of experimentally measured effects of mutations on structurally defined protein–ligand complexes (database online)
  • VariBench: benchmark database for variations (database online)
  • VariSNP: a benchmark database for variations from dbSNP (database online)
  • ANNOVAR: List of variant dbs & tools (database online)
  • CanProVar to store and display single amino acid alterations including both germline and somatic variations in the human proteome
  • 3DBIONOTES v3.0: Crossing molecular and structural biology data with genomic variations (online)
  • AWESOME: a database of SNPs that affect protein post-translational modifications (online)
  • AlloMAPS: allosteric mutation analysis and polymorphism of signaling database (online)
  • ActiveDriverDB human disease mutations and genome variation in post-translational modification sites of proteins
  • HPA human protein atlas - cancer and pathology…
  • Mouse Phenome Database : an integrative database and analysis suite for curated empirical phenotype data from laboratory mice
  • MSV3d missense mutations in 3D, human proteome
  • mutation3D functional prediction and visualization for aa substitutions on protein models and structures
  • Aquaria simplifying the generation of insight from protein structures
  • dbGaP
  • dbNSFP
  • ClinVar aggregates information about genomic variation and its relationship to human health (database online)
  • Database of Genomic Structural variation
  • European Genome-phenome Private variation
  • European Variation Archive (EVA) Public variation
  • The Human Genetic Variation Archive (HGVA)
  • Ensembl (a genome browser )
  • HGMD Disease-related gene lesions
  • HGVD Japanese genetic variation
  • Human Mutation Analysis HUMA
  • Online Mendelian In Man OMIM Human genes and genetic disorders
  • SNPeffect Characterization and annotation of SNPs
  • SNPs3D Functional effects of nonsynonymous SNPs
  • The Cancer Genome Atlas TCGA Cancer-associated mutations
  • Uniprot Protein database
  • VnD Variation and drugs
  • PDBSWS (PDB residues & Uniprot residue position mapping)
  • PROXiMATE (a database of mutant protein-protein complex thermodynamics and kinetics)

Some tools to analyze variants - Some can also be used for protein engineering

  • DDMut: predicting effects of mutations on protein stability using deep learning (online).
  • CORDAX: platform for the prediction and 3D visualization of aggregation motifs in protein sequences (sequence aggregation propensity…) (online, 2024).
  • Damietta: a comprehensive protein design toolkit (eg, saturation mutagenesis, design of novel proteins) (online) (online, 2024).
  • Frustraevo: localize and quantify the conservation of local energetic frustration for evolutionary related proteins (online, 2024).
  • Frustraevo: localize and quantify the conservation of local energetic frustration for evolutionary related proteins (standalone, 2024).
  • 3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures (standalone, 2024).
  • GlycoSHIELD-MD: simple MD pipeline to generate realistic glycoprotein models (online, 2024).
  • Varchat: Generative AI assistant for the interpretation of human genomic variations (online, 2024).
  • MMPatho: Leveraging Multilevel Consensus and Evolutionary Information for Enhanced Missense Mutation Pathogenic Prediction (online)
  • DeepAlloDriver: a deep learning-based strategy to predict cancer driver mutations (online)
  • MutateX: automated pipeline for in silico saturation mutagenesis of protein structures (standalone)
  • RosettaDDGPrediction: high-throughput mutational scans: from stability to binding (saturation mutagenesis) (standalone)
  • EvoRator2: Predicting Site-specific Amino Acid Substitutions Based on Protein Structural Information Using Deep Learning (online)
  • xProtCAS: Toolkit for Extracting Conserved Accessible Surfaces from Protein Structures (interaction with other biomolecules) (standalone)
  • xProtCAS: Toolkit for Extracting Conserved Accessible Surfaces from Protein Structures (interaction with other biomolecules) (online)
  • DDMut: predicting effects of mutations on protein stability using deep learning (standalone)
  • LambdaPP: protein structure analysis - mutation... (online)
  • DisCanVis: visualizing integrated structural and functional annotations for better understanding of the effect of cancer mutations located within disordered proteins (online)
  • Venus: Elucidating the impact of amino acid variants on protein function beyond structure destabilisation (online and also standalone)
  • ProTstab2: Prediction of Protein Thermal Stabilities (online)
  • BayeStab: Predicting Effects of Mutations on Protein Stability with Uncertainty Quantification (online)
  • BayeStab: Predicting Effects of Mutations on Protein Stability with Uncertainty Quantification (standalone)
  • Stabilizing_Proteins: A Rosetta-based webtool for predicting favorable mutations (can generate a site saturation mutagenesis heatmap…can help in case poor expression…) (online)
  • pSUFER: Assessing and enhancing foldability in designed proteins (online)
  • PCA-MutPred: Prediction of Binding Free Energy Change Upon Missense Mutation in Protein-carbohydrate Complexes (online)
  • Protposer: readily proposes protein stabilizing mutations with high positive predictive values (online)
  • EvoRator: Prediction of Residue-level Evolutionary Rates from Protein Structures Using Machine Learning (online)
  • SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning (online)
  • DisProt: improved quality and accessibility of protein intrinsic disorder annotation (online)
  • DDGun: an untrained predictor of protein stability changes upon amino acid variants (online)
  • AlignMe Membrane proteins. web server for alignment of membrane protein sequences (links to MutationExplorer...) (online and standalone)
  • patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures (online)
  • mmCSM-NA: accurately predicting effects of single and multiple mutations on protein-nucleic acid binding affinity (online)
  • LYRUS: A Machine Learning Model for Predicting the Pathogenicity of Missense Variants (standalone)
  • PSnpBind: a database of mutated binding site protein–ligand complexes constructed using a multithreaded virtual screening workflow (online and standalone)
  • DeepSVP: Integration of genotype and phenotype for structural variant prioritization using deep learning (standalone)
  • PON-Sol2: Prediction of Effects of Variants on Protein Solubility (online)
  • SCMTPP: A novel sequence-based predictor for identifying and characterizing thermophilic proteins using estimated propensity scores of dipeptides (online)
  • Voronoia 4-ever: enables fully automated analysis of the atomic packing density of macromolecules (online)
  • CIVICdb: Clinical interpretation of variants in cancer (precision medicine) (online database)
  • DeepREx-WS: A web server for characterising protein-solvent interaction starting from sequence (solvent-exposed residues) (online)
  • Leri: A web-server for identifying protein functional networks from evolutionary couplings (dataviz) (online)
  • P2T2: Protein Panoramic annoTation Tool for the interpretation of protein coding genetic variants (standalone and online)
  • PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences (online)
  • BEE: Biomedical Entity Explorer. Integrates Ensemble, PharmGKB, Genetic Home Reference, Tarbase, Mirbase, NCI Thesaurus, DisGeNET, Linked life data, UMLS, GSEA MsigDB, Reactome, KEGG, Gene Ontology, HGVD, SNPedia, and dbSNP (online)
  • Mechnetor: exploring protein mechanism and the functional context of genetic variants (online)
  • MTR3D: the server enables easy visualisation of population variation, MTR, MTR3D and MTRX scores across the entire gene and protein structure for >17,000 human genes and >42,000 alternative Ensembl and RefSeq transcripts (online)
  • ThermoScan: Semi-automatic Identification of Protein Stability Data From PubMed (Text mining, full article) (online)
  • AnnotSV: AnnotSV and knotAnnotSV: a web server for human structural variations annotations, ranking and analysis (standalone and online)
  • SWOTein: a structure-based approach to predict stability Strengths and Weaknesses of prOTEINs (identifies strong and weak residues in proteins on the basis of three types of statistical energy functions describing local interactions along the chain…) (online)
  • NNSPLICE: Splice Site Prediction by Neural Networ (online)
  • SpliceAid: a database of strictly experimentally assessed target RNA sequences in humans (online)
  • mmCSM-PPI: predicting the effects of multiple point mutations on protein-protein interactions (online)
  • usDSM: a novel method for deleterious synonymous mutation prediction using undersampling scheme (online)
  • TopSuite Web Server: A Meta-Suite for Deep-Learning-Based Protein Structure and Quality Prediction (online)
  • PheLiGe: an interactive database of billions of human genotype–phenotype associations (online)
  • TMSNP: a web server to predict pathogenesis of missense mutations in the transmembrane region of membrane proteins (online)
  • COVID-3D: An online resource to explore the structural distribution of genetic variation in SARS-CoV-2 and its implication on therapeutic development (Covid-19) (online)
  • BAlaS: fast, interactive and accessible computational alanine-scanning using BudeAlaScan (online)
  • ELASPIC2 (EL2): Combining contextualized language models and graph neural networks to predict effects of mutations (online)
  • SAAFEC-SEQ: A Sequence-Based Method for Predicting the Effect of Single Point Mutations on Protein Thermodynamic Stability (online)
  • PTMsnp: A Web Server for the Identification of Driver Mutations That Affect Protein Post-translational Modification (online)
  • SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions (PPI) (online) (or http://sbi.upf.edu/spserver/)
  • MutPred-Indel: Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome (online)
  • FireProtASR: A Web Server for Fully Automated Ancestral Sequence Reconstruction (phylogeny-based analysis; protein stability) (online)
  • GRIN DATABASE: a curated database for grin variants (online)
  • Swiss-PO.ch: tool to analyze point mutations in 3D, the focus is on oncology targets (online)
  • Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence, mutation (COVID-19) (online)
  • MPTherm-Pred: Analysis and Prediction of Thermal Stability Changes upon Mutations in Transmembrane Proteins (online)
  • UEP: an open-source and fast classifier for predicting the impact of mutations in protein-protein complexes (standalone)
  • CoV-Seq: SARS-CoV-2 Genome Analysis and Visualization (online and standalone available)
  • DynaMut2: Assessing changes in stability and flexibility upon single and multiple point missense mutations (online)
  • EVmutation: Mutation effects predicted from sequence co-variation (standalone)
  • CONAN: A web application to detect specificity determinants and functional sites by amino acids co-variation network analysis (online)
  • AlloSigMA 2: Designing allosteric effectors and to exploring allosteric effects of mutations (online)
  • LIST-S2: Taxonomy based sorting of deleterious missense mutations across species (different strategy as compared to sequence conservation alone) (online)
  • mCSM-membrane: Predicting the Effects of Mutations on Transmembrane Proteins (online)
  • SOLart: a structure-based method to predict protein solubility and aggregation (online)
  • ProTSPoM: Estimating the Effect of Single Point Mutations on Protein Thermodynamic Stability (online)
  • Probe: protein packing computation (standalone)
  • Reduce and Probe and King: tools to analyze protein structures, add hydrogen atoms, compute packing ... (standalone)
  • Occluded Surface: protein packing computation (standalone)
  • PremPS: Predicting the Effects of Mutations on Protein Stability (online)
  • SAAMBE-3D: Predicting Effect of Mutations on Protein-Protein Interactions (standalone available via github) (online)
  • FASPR: An Open-Source Tool for Fast and Accurate Protein Side-Chain Packing (standalone on github and online)
  • Rhapsody: Predicting the Pathogenicity of Human Missense Variants (standalone)
  • Rhapsody: Predicting the Pathogenicity of Human Missense Variants (online)
  • CADD: Combined Annotation Dependent Depletion. Tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome (online)
  • VIPdb: Variant Impact Predictor Database. List of tools to study variants (online)
  • VPOT: A Customizable Variant Prioritization Ordering Tool for Annotated Variants (standalone python)
  • pPerturb: Predicting Long-Distance Energetic Couplings and Mutation-Induced Stability Changes in Proteins via Perturbations (validated against a large data set of 375 mutations in 19 different proteins) (online)
  • SNP2SIM: a modular workflow for standardizing molecular simulation and functional analysis of protein variants (standalone)
  • HiPathia: tool for the interpretation of the consequences of the combined changes of gene expression levels and/or genomic mutations in the context of signalling pathways (online)
  • Modict: Convert your favorite protein modeling program into a mutation predictor, uses rmsd and others (standalone)
  • ANGDelmut: prediction and analysis of functional loss mechanisms of deleterious mutations related to amyotrophic lateral sclerosis (ALS). Full atomistic MD (not normal modes) (online)
  • ProAffiMuSeq: sequence-based method to predict the binding free energy change of protein–protein complexes upon mutation using functional classification (online)
  • SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function (online and standalone)
  • mutationTCN: deep autoregressive generative model named mutationTCN, which employs dilated causal convolutions and attention mechanism for the modeling of inter-residue correlations in a biological sequence (standalone)
  • SPDI: Services for variation data processing (online)
  • AggreRATE-Pred: A mathematical model for the prediction of change in aggregation rate upon point mutation (online)
  • EvoEF2: accurate and fast energy function for computational protein design (de novo sequence design on a given fixed protein backbone (standalone)
  • VAT: Variant Annotation Tool. A computational framework to functionally annotate variants in personal genomes using a cloud-computing environment (online)
  • PIIMS: Mutation Hotspot Scanning at the Protein-Protein Interface (online)
  • pyDockEneRes: per-residue decomposition of protein-protein docking energy (online)
  • FunSeq: functional effects of non-coding variants (online)
  • REVEL: ensemble methods that combine scores from multiple tools (Rare Exome Variant Ensemble Learner). The method was developed by combining 18 scores from 13 individual tools including MutPred, VEST, PolyPhen, SIFT and MutationTaster (online)
  • Missense3D: predicts the structural changes introduced by an amino acid substitution and is applicable to analyse both PDB coordinates and homology-predicted structures (online)
  • ENCoM: coarse-grained normal mode analysis method (can be used to investigate mutations) (standalone)
  • mCsm protein-protein: Protein-Protein Affinity Change Upon Mutation (online)
  • MutaBind: evaluates the effects of variations and disease mutations on protein-protein interactions only for soluble complexes (online)
  • iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations (standalone)
  • Genomic Position to Protein Sequence and 3D Structure at the PDB
  • VarSite: disease variants and protein structure - (includes disease propensity, and pre-mapped disease variants on interactive 3D structures - 3D-mapping of point mutation) (online)
  • HotSpot3D: An Integrated Resource for Mutation Analysis in Protein 3D Structures (3D-mapping) (online)
  • PhyreRisk: A Dynamic Web Application to Bridge Genomics, Proteomics and 3D Structural Data to Guide Interpretation of Human Genetic Variants (covers the entire proteome and displays variants on structure and sequence) - associated to Missence3D (compute also ddG) (3D-mapping of point mutation) (online)
  • VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations (3D-mapping of point mutation) (online)
  • mutfunc: Precomputed mechanistic consequences of mutations (online)
  • MISCAST: MIssense variant 3D-mapping (online)
  • MILAMP: Multiple Instance Prediction of Amyloid Proteins (online)
  • P3Fold: Fast and Flexible Coarse-grained Prediction of Protein Folding Routes using Ensemble Modelling and Evolutionary Sequence Variation (online)
  • ProtFus: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins (online)
  • svtools: population-scale analysis of structural variation (standalone)
  • BorodaTM: Prediction of disease-associated mutations in the transmembrane regions of proteins with known 3D structure (online)
  • MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains (online)
  • Simple ClinVar: an interactive web server to explore and retrieve gene and disease variants aggregated in ClinVar database (online and standalone perl script)
  • SNP2SIM: a modular workflow for standardizing molecular simulation and functional analysis of protein variants (standalone)
  • DNAscan: personal computer compatible NGS analysis, annotation and visualisation (standalone)
  • Interactome INSIDER: a structural interactome browser for genomic studies
  • VarQ: A Tool for the Structural and Functional Analysis of Human Protein Variants (online)
  • TKSA-MC: A Web Server for rational mutation through the optimization of protein charge interactions (Tanford-Kirkwood Surface Accessibility model) (standalone on GitHub)
  • AIMMS: a web server dedicated for prediction of drug resistance on protein mutation (online)
  • MolArt: MOLecular STructure AnnotatoR, enables users to view annotated protein sequence (including variation data from large scale studies) and overlay the annotations over a corresponding experimental or predicted protein structure
  • VarAFT: disease-causing variants annotation
  • ELASPIC: proteome-wide structure-based prediction of mutation effects on protein stability and binding affinity (online)
  • MoRFpred: Predicting Functions of Disordered Proteins (online)
  • shiny-pred: a server for the prediction of protein disordered regions (online)
  • GDA :a web-based tool for Genomics and Drugs integrated analysis
  • SNPnexus :assessing the functional relevance of genetic variation to facilitate the promise of precision medicine
  • RFAmyloid: Server for Predicting Amyloid Proteins
  • DynaMut :predicting the impact of mutations on protein conformation, flexibility and stability
  • IMPACT : oncology database integrating molecular profiles with actionable therapeutics
  • KRDS a web server for evaluating drug resistance mutations in kinases by molecular docking
  • Variant Effect Predictor (VEP) VEP (Ensembl) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions
  • G2S A web-service for annotating genomic variants on 3D protein structures
  • Disulfide by Design 2.0 (DD2) (a web-based tool for disulfide engineering in proteins)
  • TANGO A computer algorithm for prediction of aggregating regions in unfolded polypeptide chains
  • FireProt: automated design of thermostable proteins
  • ADEPTUS discovery and analysis tool based on expression and mutation data from many diseases (eg., cancer)
  • Zebra a web server for bioinformatic analysis of diverse protein families
  • visualCMAT Helps to select and interpret correlated mutations/co-evolving residues in protein families (is integrated with the Mustguseal web-server capable of constructing large structure-guided sequence alignments of protein families and superfamilies)
  • MISTIC2: comprehensive server to study coevolution in protein families - circular dataviz (online)
  • MAESTROweb :a web server for structure based protein stability prediction
  • Delta (DNA, Web-based 3D genome visualization and analysis platform)
  • pStab (Prediction of Stable Mutants (single- or multiple-point substitutions of charged residues, Unfolding Curves, Stability Maps and Protein Electrostatic Frustration)
  • Folding RaCe (method for predicting changes in protein folding rates upon point mutations (two-state folders))
  • ENTPRISE: An Algorithm for Predicting Human Disease-Associated Amino Acid Substitutions from Sequence Entropy and Predicted Protein Structures
  • 3D Hotspots: mutation hotspots in protein chains (cancer) (online)
  • BeAtMuSiC: protein-protein affinity upon mutation (online)
  • BindProfX: protein-protein affinity upon mutation (online)
  • HOPE: 3D visualization, seq. and structural features (online)
  • INPS-3D: protein stability (online)
  • KD4v: phenotypic effect (online)
  • MOKCa: mutation hotspots in protein domains (cancer) (online)
  • MultiMutate: protein stability (online)
  • MUpro: protein stability from sequence (online)
  • MutationAligner: Somatic mutation hotspots in protein domains in cancer (online)
  • SAAPdap: Single Amino Acid Polymorphism data analysis pipeline - sequence or 3D (online)
  • SDS: SDS Pharmacogenes is a score that represents the number of structural disturbances caused by an amino acid variant in a pharmacogene (online)
  • STRUM: mutant stability change (online)
  • SuSPect: phenotypic effect (online)
  • VIPUR: Variant Interpretation and Prediction Using Rosetta (standalone)
  • ws-SNP&GO3d: phenotypic effect 2D and 3D (online)
  • PDBFlex: database explores the intrinsic flexibility of protein structures by analyzing structural variations between different depositions and chains in asymmetric units of the same protein in PDB. It allows to easily identify regions and types of structural flexibility present in a protein of interest (online)
  • cBioPortal: mapping and 3D visualization - cancer genomics (online)
  • JalView: multiple seq. alignment and annotation visualization (online)
  • CADD: Combined Annotation Dependent Depletion. A tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome (sequence) (online)
  • CAROL: CAROL is a combined functional annotation score of non-synonymous coding variants. PolyPhen-2 + SIFT (standalone)
  • CHASM: CHASM (Cancer-specific High-throughput Annotation of Somatic Mutations). SNV-Box is a database of pre-computed features of all possible amino acid substitutions at every position of the annotated human exome. Users can rapidly retrieve features for a given protein amino acid substitution for use in machine learning (standalone)
  • Evolutionary Action: A formal perturbation equation between genotype and phenotype determines the evolutionary action of protein coding variations on fitness (online)
  • iFish2: Integrated transcript/gene/gene-family customized classifiers for Functional Inference of non-synonymous SNVs in Human genome together with genetic data fusion (online)
  • MutPred-LOF: Frameshift and nonsense mutation pathogenicity and effect on protein structure and function (sequence) (standalone)
  • VAAST2: Variant Annotation, Analysis and Search Tool (sequence) (online)
  • nsSNPAnalyzer (predicting disease-associated nonsynonymous single nucleotide polymorphisms)
  • MutationTaster (sequence)
  • dSysMap (Mapping of Human disease-related mutations at the systemic level, structural interactome)
  • Hotspot3d (structure)
  • PISA (PDBePISA, interactive tool for the exploration of macromolecular interfaces)
  • SnpEff - SnpSift (Genetic variant annotation and effect prediction toolbox)
  • Auto-Mute 2.0 Sequence and structure based (stability change)
  • CScape : predicts oncogenic single-point mutations in the cancer genome
  • FATHMM-XF : accurate prediction of pathogenic point mutations via extended features
  • webPSN v2.0: A Webserver to Infer Fingerprints of Structural Communication in Biomacromolecules (proteins and nucleic acids, along the line of residue interaction networks but on dynamic system see also the RING server for static computations) (online)
  • ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism (online)
  • SAAFEC: An online application for calculating folding free energy changes in proteins caused by missense mutations (online)
  • DUET: stability change by combining two approaches
  • CUPSAT Structure based (stability change)
  • I-Mutant2.0 Sequence and structure based (stability change)
  • MuPro Sequence and structure based (stability change)
  • NeEMO Residue interaction networks (stability change)
  • PoPMuSiC 2.1 Structure based (stability change)
  • FATHMM Sequence based
  • MAPP Sequence based
  • Meta-SNP Consensus classifier
  • MuD Sequence and structure based
  • MutPred2 Sequence and structure-based
  • PANTHER-PSEP Sequence based
  • Parepro Sequence-based
  • PolyPhen-2 Sequence and (partially)-structure based
  • SIFT Sequence-based
  • SNAP Sequence-based
  • SNPs&GO Sequence and structure based
  • VAPOR (Variant Analysis Consensus classifier)
  • G23D
  • PredictSNP2 (consensus)
  • Cancer3D
  • MANORAA
  • mCSM-lig
  • Plot protein: visualization of mutations
  • ESBRI (salt bridges, electrostatics)
  • PROVEAN (Sequence and structure based)
  • StructMAn
  • PsychoProt
  • Pharos (druggable genome - TCRD - (target central resource database))
  • BindProf : deltadeltaG on PPI interface, needs a list of residue
  • DrugScorePPI (deltadeltaG on PPI interface) (systematic search, hotspots)
  • PredHS (protein-protein interaction hotspots (sort of deltadelta G)
  • wANNOVAR: ANNOVAR is a rapid, efficient tool to annotate functional consequences of genetic variation from high-throughput sequencing data
  • dbSNP
  • 1000 genomes project
  • mutLBSgeneDB (mutated binding pockets)
  • Genomics, Evidence, Neoplasia, Information, Exchange (GENIE)
  • MSV3d
  • DaMold
  • INPS-MD (predict stability)
  • ABCMdb (mutations in ATP binding cassette proteins - ADMET)
  • INTAA: Amino Acid Interaction (INTAA) web server. Calculation of the residue Interaction Energy Matrix for any protein structure. Aims to identify key residues within protein structures which contribute significantly to the stability of the protein (online)
  • NewProt (protein engineering portal, mutation via HOPE & the Hotspot Wizard...)
  • PON-P2 predicts the pathogenicity of aa changes
  • VEST: Variant Effect Scoring Tool
  • MuPIT: map variant positions in 3D
  • CRAVAT: cancer-related analysis of variants toolkit
  • SODA (protein solubility)
  • FELLS (fast estimator of latent local structure)
  • DEOGEN2: predictor of missense SVNs
  • MutationAssessor
  • GenProBiS (mapping variants to protein binding sites)
  • mCSM-DNA: aa changes on protein-nucleic acids
  • PhD-SNPg (coding and non-coding regions)
  • PMut
  • Prosat+ visualize 3D structure, sequences, fetch related sequence, (protein structure annotation online)
  • SIFTS (integrate 3D structure, function, taxonomy & sequence, PDB-UniProt mapping)
  • VCF.Filter (disease-linked genetic variants from sequencing data)
  • MAESTRO (multi agent stability prediction upon point mutations)
  • mCSM (effect of mutations on stability, PPI, protein-DNA)
  • SDM (impact of mutations on protein stability)
  • Protein-Sol (predict protein solubility from sequence)
  • Solubis (reduce protein aggregation through mutation, check for peptides)
  • Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubility (online and standalone on the way)
  • AGGRESCAN3D (A3D): prediction of aggregation (proteins)
  • Aggrescan3D: python package for structure-based prediction of protein aggregation (standalone)
  • Protter (interactive protein feature visualization)
  • Protein-Sol: Web-based display of protein surface and pH-dependent properties for assessing the developability of biotherapeutics (with 3D data) (online)
  • MutaGene (explore cancer mutations)
  • Variant Ranker (according to functional significance)
  • SCooP (protein stability curves as a function of the temperature, maybe not fully for point mutation but related)
  • MutaNET (analysis of genomic mutations in gene regulatory networks)
  • Spliceman2: predicts defects in pre-mRNA splicing

Peptide design

  • POSEIDON: The Peptidic Objects SEquence-based Interaction with cellular DOmaiNs website allows the user to input solely a peptide sequence and attain an in silico prediction for its uptake value in different cell lines. The tool deals with Cell-penetrating peptides (CPPs). The site provides a database and a ML Predictor that should help advancing research on CPP-related topics. POSEIDON was published in February 2024 by Preto et al., Journal of Chemoinformatics (online).
  • BrainPepPass: A Framework Based on Supervised Dimensionality Reduction for Predicting Blood-Brain Barrier-Penetrating Peptides (standalone)
  • BBB-PEP-prediction:: identification of blood–brain barrier peptides (standalone)
  • camsolptm: Sequence-based prediction of the intrinsic solubility of peptides containing non-natural amino acids (online)
  • pyPept: a python library to generate atomistic 2D and 3D representations of peptides (Sept 2023) (standalone)
  • NeuroPred-PLM: an interpretable and robust model for neuropeptide prediction by protein language model (standalone)
  • PEP-FOLD4: a pH-dependent force field for peptide structure prediction in aqueous solution (online)
  • PepSim: T-cell cross-reactivity prediction via comparison of peptide sequence and peptide-HLA structure (online)
  • MaSIF-seed: De novo design of protein interactions with learned surface fingerprints (PPI peptides) (standalone)
  • peptide-dashboard: Serverless Prediction of Peptide Properties with Recurrent Neural Networks (sequence-based solubility predictor, MahLooL, resistance to nonspecific interactions, hemolysis) (standalone)
  • UniDL4BioPep: a universal deep learning architecture for binary classification in peptide bioactivity (standalone)
  • UniDL4BioPep: a universal deep learning architecture for binary classification in peptide bioactivity (online)
  • CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides (online)
  • NeuroPred-PLM: an interpretable and robust model for neuropeptide prediction by protein language model (online)
  • Propedia v2.3: A novel representation approach for the peptide-protein interaction database using graph-based structural signatures (online)
  • BBPpredict: a Web Service for Identifying Blood-Brain Barrier Penetrating Peptides (BBB) (online)
  • MDockPeP2: Predicting Protein-Peptide Complex Structures by Accounting for Peptide Flexibility and the Physicochemical Environment (standalone)
  • Pep-Whisperer: Inhibitory Peptide Design (online)
  • ATLIGATOR: analyse protein-protein or protein-peptide interactions (Oct 2023) (online)
  • ATLIGATOR: analyse protein-protein or protein-peptide interactions (standalone)
  • pIChemiSt: Calculation of Isoelectric Points of Modified Peptides (standalone)
  • B3PP: Improved prediction and characterization of blood-brain barrier (BBB) penetrating peptides using estimated propensity scores of dipeptides (online)
  • CSM-peptides: A computational approach to rapid identification of therapeutic peptides (online)
  • ProAll-D: protein allergen detection using long short term memory - a deep learning approach (data)
  • PDAUG: a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling (standalone)
  • InterPepScore: a deep learning score for improving the FlexPepDock refinement protocol (online)
  • AMPBenchmark: Benchmarks in antimicrobial peptide prediction are biased due to the selection of negative data (online)
  • AMPBenchmark: Benchmarks in antimicrobial peptide prediction are biased due to the selection of negative data (datasets)
  • PreTP-Stack: prediction of therapeutic peptide based on the stacked ensemble learning (online)
  • pyDockEneRes: per-residue decomposition of protein-protein docking energy (online)
  • PPI-Affinity: Prediction and Optimization of Protein-Peptide and Protein-Protein Binding Affinity (online)
  • FastTargetPred-Chembl29-dataset: A new ChEMBL dataset for FastTargetPred and target fishing for an exhaustive list of linear tetrapeptides (chemogenomics) (dataset)
  • DRIFT: Whole proteome mapping of compound-protein interactions (online)
  • PeptideDesignGA: Peptide Design Genetic Algorithm (PDGA) (standalone)
  • POPPIT: Exploration of target spaces in the human genome for protein and peptide drugs (online)
  • ViralFP: A Web Application of Viral Fusion Proteins, peptides (online)
  • PepSeA: Peptide Sequence Alignment and Visualization Tools to Enable Lead Optimization (standalone)
  • Antifungal: Large-Scale Screening of Antifungal Peptides Based on Quantitative Structure-Activity Relationship (online)
  • CycPeptPPB: Plasma protein binding prediction focusing on residue-level features and circularity of cyclic peptides by deep learning (standalone)
  • ToxIBTL: prediction of peptide toxicity based on information bottleneck and transfer learning (online)
  • Defpred: predicts the presence of Defensins in given query protein sequence (online)
  • UMPred-FRL: A New Approach for Accurate Prediction of Umami Peptides Using Feature Representation Learning (online)
  • STM: Sense the moment: A highly sensitive antimicrobial activity predictor based on hydrophobic moment (online)
  • PDGA-MAP4_AP: Peptide Design Genetic Algorithm (PDGA) (standalone)
  • Deep-AVPpred: Artificial intelligence driven discovery of peptide drugs for viral infections (online)
  • sAMP-PFPDeep: Improving accuracy of short antimicrobial peptides prediction using three different sequence encodings and deep neural networks (standalone)
  • AHTPDB: a comprehensive platform for analysis and presentation of antihypertensive peptides (several thousand peptides with IC50 values) (online)
  • finDr: A web server for in silico D-peptide ligand identification. Performs molecular docking (with Vina) to virtually screen a library of helical 12-mer peptides extracted from the RCSB Protein Data Bank (PDB) for their ability to bind to the target (online)
  • THPdb: comprehensive database based on approved and approved/investigational therapeutic peptides compiling important information about these peptides (online)
  • CancerPPD: provides detailed information related to experimentally verified anticancer peptides (ACPs) and proteins (online)
  • PEPlife: peptide collection (online)
  • SATPdb: database of structurally annotated therapeutic peptides curated from twenty public domain peptide databases (online)
  • StraPep: a structure database of bioactive peptides (online)
  • Bioactive peptide databases: list 32 databases (online)
  • PepBank: a database of peptides based on sequence text mining and public peptide data sources (online)
  • Brainpeps: a resource of blood-brain barrier properties of peptides (online)
  • EROP-Moscow: Endogenous Regulatory OligoPeptide knowledgebase (online)
  • PRM: contains 500 domains from 82 PRM families and 387 proteins (online)
  • DFBP: Database of food-derived bioactive peptides (online)
  • Peptipedia: a comprehensive database for peptide research supported by Machine Learning approach (standalone)
  • Peptipedia: a comprehensive database for peptide research supported by Machine Learning approach (online)
  • Propedia: a database for protein–peptide identification based on a hybrid clustering algorithm (online)
  • InterPepRank: Assessment of Docked Peptide Conformations by a Deep Graph Network (online and standalone)
  • InterPep1.0: Predicting protein-peptide interaction sites using distant protein complexes as structural templates (online)
  • 502 protein-peptide complexes in 3D: dataset available (online)
  • DRAMP 3.0: an enhanced comprehensive data repository of antimicrobial peptides (online database)
  • PepDraw: Tool to draw peptide in 2D (online)
  • AI4AMP: an Antimicrobial Peptide Predictor Using Physicochemical Property-Based Encoding Method and Deep Learning (online)
  • PepSMI: Convert Peptide to SMILES string (online)
  • BIOPEP-UWM database: Database of Bioactive Peptides (online)
  • CycloPs: A Cyclic Peptide Library Generator... return smiles strings (standalone)
  • Dendrimer builder: Build peptides and modified peptides and return smiles strings (online)
  • StarPepDB: integrated graph database holding bioactive peptides and metadata from a large variety of biological data sources (database and software package) (standalone)
  • DBAASP v3: database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics (online)
  • Peptipedia: application and a comprehensive database for peptide research supported by Machine Learning approach (standalone)
  • APPTEST: novel protocol for the automatic prediction of peptide tertiary structures (online)
  • ConjuPepDB: a database of peptide–drug conjugates (online)
  • PreTP-EL: prediction of therapeutic peptides based on ensemble learning (online)
  • PSSP-MVIRT: peptide secondary structure prediction based on a multi-view deep learning architecture (sequence based) (online)
  • PSSP-MVIRT: peptide secondary structure prediction (standalone) (dataset needed - ask the authors)
  • ENNAVIA: neural networks for antiviral and anti-coronavirus activity prediction for therapeutic peptides (online)
  • AMPDiscover: Alignment-Free Antimicrobial Peptide Predictors (online)
  • ANuPP: Tool to Predict Aggregation Nucleating Regions in Peptides and Proteins (online)
  • Iampraac: Amino Acid Reduction Can Help to Improve the Identification of Antimicrobial Peptides and Their Functional Activities (online)
  • BChemRF-CPPred: Predicting cell-penetrating peptides using machine learning algorithms and navigating in their chemical space (online)
  • PepTherDia: database and structural composition analysis of approved peptide therapeutics and diagnostics (online)
  • ACCLUSTER: predicts peptide binding sites on a given protein structure by clustering chemical interactions between amino acid probes and the protein receptor (online)
  • MDockPeP: predicts protein-peptide complex structures starting with the protein structure and peptide sequence (online)
  • ENNAACT: neural networks for anticancer activity classification for therapeutic peptides (online)
  • BERT4Bitter: a bidirectional encoder representations from transformers (BERT)-based model for improving the prediction of bitter peptides (online)
  • C2Pred: A sequence-based tool for identifying cell-penetrating peptides (online)
  • CellPPD: Designing of Cell Penetrating Peptides (online)
  • Protparam: tool which allows the computation of various physical and chemical parameters for a given protein (online)
  • PepCalc: Peptide property calculator (e.g., water solubility) (online)
  • Heliquest: hydrophobicity, and polar-, non-polar-, uncharged- and charged residues, membrane binding potential (online)
  • ToxinPred: Determination of toxicity (online)
  • AllergenFP: prediction allergen (online)
  • HemoPI: hemolytic property of peptides (online)
  • ProtLifePred: The protein or peptide half-life (online)
  • HLP: predicting half-life of peptides in intestine-like environment (online)
  • BBPpred: blood-brain barrier peptides prediction (input sequence) (online)
  • CPMG: Composite Peptide Macrocycle Generator (standalone)
  • ConfBuster++: an RDKit port of the open-source software ConfBuster. Generate 3D conformations of library members (standalone)
  • EpiDope: A Deep Neural Network for linear B-cell epitope prediction (standalone)
  • DStabilize: A Web Resource to Generate Mirror Images of Biomolecules (convert between L-proteins and D-proteins and for sequence reversal of D-peptides) (online)
  • COVID-19 Docking Server: An interactive server for docking small molecules, peptides and antibodies against potential targets of COVID-19 (online)
  • HAPPENN: Novel Tool for Hemolytic Activity Prediction for Therapeutic Peptides Which Employs Neural Networks (online)
  • PepSet: A benchmark consisting of 185 protein-peptide complexes with peptide length ranging from 5 to 20 residues (dataset) (standalone)
  • NetMHCIIpan-4.0: Improved Predictions of MHC Antigen Presentation by Concurrent Motif Deconvolution and Integration of MS MHC Eluted Ligand Data (online)
  • NetMHCpan-4.1: Improved Predictions of MHC Antigen Presentation by Concurrent Motif Deconvolution and Integration of MS MHC Eluted Ligand Data (online)
  • InteractomeSeq: A web server for the identification and profiling of domains and epitopes from Phage Display and Next Generation Sequencing data (online)
  • PeptiMap: Detection of peptide-binding sites on protein surfaces (online)
  • PepCoGen: A tool for generating all the possible combinations that a particular peptide sequence can acquire owing to its physiochemical properties (online)
  • InterPep2: Global Peptide-Protein Docking Using Interaction Surface Templates (standalone)
  • PDGA: In drug discovery, one uses chemical space as a concept to organize molecules according to their structures and properties. One often would like to generate new possible molecules at a specific location in the chemical space marked by a molecule of interest. This tool is capable of producing peptide sequences of various topologies (linear, cyclic/polycyclic, or dendritic) in proximity of any molecule of interest in a chemical space defined by macromolecule extended atom-pair fingerprint (MXFP), an atom-pair fingerprint describing molecular shape and pharmacophores (standalone)
  • modlAMP: This is a Python 3 package designed for working with peptides, proteins or any sequence of natural amino acids (standalone)
  • APD: The Antimicrobial Peptide Database (APD) contains 3156 antimicrobial peptides from six kingdoms (349 bacteriocins/peptide antibiotics from bacteria, 5 from archaea, 8 from protists, 20 from fungi, 352 from plants, and 2342 from animals, including some synthetic peptides, some acts on cancer, are protease inhibitors, ion channel inhibitors...tools to improve peptides as well) (online)
  • StraPep: a structure database of bioactive peptides (online)
  • FoldamerDB: A database of peptidic foldamers, non-natural oligomers that mimic the structural behaviour of natural peptides, proteins and nucleotides by folding into a well-defined 3D conformation in solution (database online)
  • ProtDCal-Suite: numerical codification and functional analysis of proteins. Set of machine learning-based methods for studying proteins, PPI-Detect for PPI and protein-peptides... (online)
  • DockThor: Free Web Server for Protein-ligand Docking, the V2 version has been shown efficient to dock peptides (online)
  • ELM: Eukaryotic Linear Motif (ELM) resource (online)
  • Short Peptides in SMILES: Small peptides in SMILES and three-dimensional formats for virtual screening campaigns (database)
  • SATPdb: database of structurally annotated therapeutic peptides (online)
  • Major Peptide Resources: peptide databases and tools (online)
  • PepBank: database of peptides based on sequence text mining and public peptide data sources. Only peptides that are 20 amino acids or shorter are stored (online)
  • PeptideAtlas: a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments (online)
  • WALTZ-DB 2.0: open-access database providing information on experimentally determined amyloid-forming hexapeptide sequences (online)
  • MODPEP: fast ab initio structure prediction of linear peptides or disorder proteins (online)
  • P3Fold: Fast and Flexible Coarse-grained Prediction of Protein Folding Routes using Ensemble Modelling and Evolutionary Sequence Variation (online)
  • ADCP: AutoDock CrankPep: Combining folding and docking to predict protein-peptide complexes (standalone)
  • PepVis: An integrated Peptide Virtual Screening pipeline for ensemble and flexible docking protocols (standalone)
  • PIPER-FlexPepDock: High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock (online)
  • PepX: Fast and accurate prediction of peptide docking (standalone)
  • PeptoGrid: Rescoring Function for AutoDock Vina to Identify New Bioactive Molecules from Short Peptide Libraries (standalone)
  • SPOT-peptide: Template-based prediction of peptide-binding proteins and peptide-binding sites (online)
  • SolyPep: Random peptide library generation, accounting or not for solubility, and preparing for docking (online)
  • MDockPeP: An ab-initio protein-peptide docking server (online)
  • PepBDB: a comprehensive structural database of biological peptide–protein interactions (online)
  • IEDB: Immune epitope database and analysis (this open resource holds data on more than 900,000 epitopes, products of the curation of immunologic assays) (online)
  • AllerTOP: Bioinformatics tool for allergenicity prediction (online)
  • HPEPDOCK:blind peptide-protein docking based on a hierarchical algorithm (online)
  • PlifePred:In silico approaches for predicting the half-life of natural and modified peptides in blood (online)
  • SPRINT-str:Structure-based Prediction of Protein-peptide Binding Regions using Random Forest (online)
  • Pep-Fold (including cyclic) (PEPFOLD) (online)
  • SPIDR:small-molecule peptide-influenced drug repurposing. SPIDR is integrated into DockoMatic v 2.1. The tool contains an intuitive graphical interface for peptide mutant screening workflow and facilitates mapping, clustering, and searching of local molecular databases. SPIDR incorporates the SimSearcher utility, which generates shape distribution signatures of molecules and employs multi-level K-means clustering to insure fast database queries (standalone)
  • Amp scanner: Deep Learning Improves Antimicrobial Peptide Recognition (Antimicrobial Peptide Scanner), online
  • FlexPepDock: a high-resolution peptide-protein docking (refinement) protocol for the modeling of peptide-protein complexes, implemented in the Rosetta framework (online)
  • MLACP: machine-learning-based prediction of anticancer peptides (online)
  • PEP-SiteFinder: A service to identify candidate protein-peptide interaction sites (online)
  • PepCrawler: A fast RRT-based algorithm for high-resolution refinement and binding-affinity estimation of peptide inhibitors (online)
  • CABS-dock: server for flexible protein-peptide docking (online)
  • CABS-dock standalone: a toolbox for flexible protein-peptide docking (standalone)
  • PEPOP: mapping of discontinuous epitopes (you may need to contact the authors to get a password)
  • PepSite: prediction of peptide-binding sites from protein surfaces (online)
  • Pepsite2: prediction of peptide-binding sites from protein surfaces (online)
  • GalaxyPepDock: Protein-peptide docking based on interaction similarity (online)
  • BioPepDB repository of bioactive peptides (online)
  • PhyreStorm (find related structure in the PDB) online
  • CoinFold (protein folding using sequence as input) online
  • PEP-FOLD3 (peptide and complexes) online
  • Peptiderive (Derive peptide inhibitors from PPi) online
  • pepMMsMIMIC (peptide to small molecule) online
  • PEPstrMOD: server predicts the tertiary structure of small peptides with sequence length varying between 7 to 25 residues (online)
  • HADDOCPBSA: HADDOCK standalone
  • PLOP (cyclic peptides) standalone
  • PinaColada: Peptide-Inhibitor Ant Colony Ad-hoc Design Algorithm (online)
  • PRODIGY: PRODIGY (PROtein binDIng enerGY prediction) is a collection of web services focused on the prediction of binding affinity in biological complexes as well as the identification of biological interfaces from crystallographic one (PPI, protein-ligand, biological interface) (online)
  • Smiles2Monomers: a software to infer monomeric structure of polymers from their atomic structure (online standalone)
  • TAGSFREE: Encoding System for Combinatorial Peptide Libraries (standalone)
  • CPPsite (database):cell penetrating peptides online
  • JPred: A Protein Secondary Structure Prediction Server (online)
  • PSIPred: Protein Sequence Analysis Workbench (online)
  • PEP2D: Peptide Secondary Structure Prediction server (online)
  • PEPlife (database of half life) online
  • Rosetta: computational modeling and analysis of protein structures (online)
  • trRosetta: fast and accurate protein structure prediction (powered by deep learning, predict the inter-residue geometries, including distance and orientation and the predicted geometries are then transformed as restraints to guide the structure prediction on the basis of direct energy minimization) (online and standalone)
  • QUARK: ab initio protein structure prediction and protein peptide folding (online)
  • MUSTER: protein threading algorithm to identify the template structures from the PDB library (online)
  • SEGMER: segmental threading algorithm designed to recoginzing substructure motifs from the Protein Data Bank (PDB) library (online)
  • LOMETS: web service for protein structure prediction (online)
  • Cluspro: protein-protein docking and others inlcuding Template-Based Modeling (online)
  • Anti-inflammatory proteins/peptides (antiinflam) online
  • ACCLUSTER for Peptide Binding Site Prediction, online
  • NNAlign (identification linear motifs, amino acid or nucleotide, and align) online
  • GibbsCluster: unsupervised clustering and alignment of peptide sequences, online
  • ClusPro PeptiDock online
  • pepATTRACT (peptide-protein docking) online
  • LoopFinder (investigates loop-mediated PPI) online
  • CPPred-RF (predictor cell-penetrating peptides) online
  • Protein-Sol (predict protein solubility from sequence) online
  • Solubis (reduce protein aggregation through mutation, check for peptides) online
  • AGGRESCAN3D (A3D): prediction of aggregation (proteins) online
  • miPepBase database of Experimentally Verified Peptides Involved in Molecular Mimicry, online
  • Minimotif Miner 4 a million peptide minimotifs and counting, online
  • Protter (interactive protein feature visualization) online
  • DINC 2 (A New Protein-Peptide Docking Webserver) online

Compound collections, medicinal drugs & pharmacology/protein databases

  • Natural product subsets (DIFACQUIM): Natural product datasets (diverse with Python code to generate diversity) (dataset)
  • PeruNPDB: the Peruvian Natural Products Database for in silico drug screening (database)
  • KIBA: An integrated drug–target bioactivity matrix across 52498 chemical compounds and 467 kinase targets (dataset)
  • npatlas: The Natural Products Atlas 2.0: A Database of Microbially-Derived Natural Products (online)
  • TCMSID: a simplified integrated database for drug discovery from traditional chinese medicine (online)
  • PROTAC-DB 2.0: an updated database of PROTACs (online)
  • MP-VHPPI: Meta predictor for viral host protein-protein interaction prediction in multiple hosts and viruses (online)
  • DrugMAP: molecular atlas and pharma-information of all drugs (online)
  • DRESIS: the first comprehensive landscape of drug resistance information (online)
  • ProtCAD: a comprehensive structural resource of protein complexes (online)
  • ChemPert: database consisting of 82 270 transcriptional signatures in response to 2566 unique compounds across 167 normal cell types/lines and tissues, as well as the protein targets of 57,818 chemical compounds (online)
  • CovInter: The Interaction data between CoronaVirus RNAs and host Proteins (COVID19) (online)
  • e-TSN: an interactive visual exploration platform fortarget–disease knowledge mapping from literature (online)
  • COVIDpro: Database for mining protein dysregulation in patients with COVID-19 (online)
  • DDrare: database that provides information on drugs in clinical trials, and drug target genes and pathways, related to the intractable diseases (mostly rare diseases) designated by the Ministry of Health, Labour and Welfare (MHLW), Japan (online)
  • RSDB: A rare skin disease database to link drugs with potential drug targets for rare skin diseases (online)
  • SYNBIP: synthetic binding proteins for research,diagnosis and therapy (online)
  • BrainBase: a curated knowledgebase for brain diseases (online)
  • DO: The Human Disease Ontology database (online)
  • MAPIYA: contact map server for identification and visualization of molecular interactions in proteins and biological complexes (online)
  • deepHPI: a comprehensive deep learning platform for accurate prediction and visualization of host-pathogen protein-protein interactions (online)
  • CDEK: Clinical Drug Experience Knowledgebase (online)
  • MolData: A Molecular Benchmark for Disease and Target Based Machine Learning (standalone)
  • POPPIT: Exploration of target spaces in the human genome for protein and peptide drugs (online)
  • PADFrag: A Database Built for the Exploration of Bioactive Fragment Space for Drug Discovery (online)
  • Neo4covid19: A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research (online)
  • IUPHAR: expert-driven guide to pharmacological targets and the substances that act on them (online)
  • OrthoDB: evolutionary and functional annotations of orthologs (online)
  • Channelpedia: a knowledge-based framework centered on genetically expressed ion channel models (online)
  • RBP2GO: a comprehensive pan-species database on RNA-binding proteins, their interactions and functions (online)
  • TCDB: The Transporter Classification Database (online)
  • MGD: community model organism knowledgebase for the laboratory mouse (online database)
  • INTEDE: interactome of drug-metabolizing enzymes (online)
  • KinCoRe: A web resource for protein kinase sequence, structure and phylogeny (online)
  • DISEASES: disease-gene associations mined from the literature (online)
  • GproteinDb: The G protein database (online)
  • Antiviral Combination DB: Search for synergistic antiviral drug combinations from integrative resource (Covid-19) (database online)
  • COVIDium: a COVID-19 resource compendium (online)
  • COVID19db: a comprehensive database platform to discover potential drugs and targets of COVID-19 at whole transcriptomic scale (online database)
  • OlfactionBase: A repository to explore odors, odorants, olfactory receptors and odorant-receptor interactions (online)
  • SistematX Web Portal: Natural products and their secondary metabolites are promising starting points for the development of drug prototypes and new drugs. Plant secondary metabolite database (online database)
  • CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations (standalone and online)
  • EU vet drugs: Centralised veterinary medicinal products by ATC code (online)
  • EU med drugs: Centralised medicinal products for human use by ATC code (online)
  • CMNPD: a comprehensive marine natural products database towards facilitating drug discovery from the ocean (online)
  • DREIMT: a drug repositioning database and prioritization tool for immunomodulation (online)
  • DRUGPATH: The Drug Gene Pathway Meta-Database (online)
  • MarkerDB: consolidates information on all known clinical and a selected set of pre-clinical molecular biomarkers into a single resource (online)
  • PPDB: Pesticide Properties Database (online)
  • HPIDB: Host-Pathogen Interaction Database (online)
  • PathoPhenoDB: linking human pathogens to their phenotypes in support of infectious disease research (online)
  • EpiGraphDB: a database and data mining platform for health data science (online)
  • Viruses.STRING: a virus–host protein–protein interaction database (online)
  • Brenda: The comprehensive enzyme information system (online)
  • MMpI: A WideRange of Available Compounds of Matrix Metalloproteinase Inhibitors (online)
  • Paired Omics Data Platform: community-based initiative standardizing links between genomic and metabolomics data in a computer readable format to further the field of natural products discovery (online)
  • CoV-Seq: New Tool for SARS-CoV-2 Genome Analysis and Visualization (Covid-19) (online)
  • Virus-CKB: An integrated bioinformatics platform and analysis resource for COVID-19 research (online)
  • COVID-19 preVIEW: Semantic Search to Explore COVID-19 Research Preprints (text mining) (online)
  • COKE: COVID-19 Knowledge Extractor, A Tool and a Web Portal to Extract Drug - Target Protein Associations from the CORD-19 Corpus of Scientific Publications on COVID-19, text-mining (online)
  • MICHA: Minimal information for Chemosensitivity assays: A next-generation pipeline to enable the FAIRification of drug screening experiments (at present Cancer and COVID-19) (online)
  • CoV-RDB: Coronavirus Antiviral Research Database: An Online Database Designed to Facilitate Comparisons between Candidate Anti-Coronavirus Compounds (COVID-19) (online)
  • COVID-19 Molecular Structure and Therapeutics Hub: aggregating critical information to accelerate drug discovery for the molecular modeling and simulation community (online)
  • canSAR Coronavirus Discovery resource: collates multiple molecular and clinical data types related to COVID-19 (online)
  • CORD-19: the COVID-19 open research dataset: integrates papers from several sources (online)
  • CORDITE: CORona Drug InTEractions database collects and aggregates data for SARS-CoV-2 from: PubMed MedRxiv BioRxiv ChemRxiv ClinicalTrials.gov (COVID-19) (online)
  • Targeting2019-nCoV: COVID-19 preclinical studies, GHDDI Info Sharing Portal. 82 coronavirus-human interactions with experimental evidence are provided by PHISTO, involving 33 human proteins and 21 coronavirus proteins (online)
  • sars3d: SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets (oligomeric modelling, binding pocket prediction, mutation analysis, docking compounds). SARS-CoV-2 Proteome-3D Analysis (COVID-19) (online)
  • CoV3D: a database of high resolution coronavirus protein structures (with sequences, variants…) (COVID-19) (online)
  • GESS: a database of global evaluation of SARS-CoV-2/hCoV-19 sequences (COVID-19) (online)
  • ViruSurf: a large public database of viral sequences and integrated and curated metadata from heterogeneous sources (RefSeq, GenBank, COG-UK and NMDC) (COVID-19) (online)
  • COVID19 Drug Repository: text-mining the literature in search of putative COVID19 therapeutics (online)
  • LitCovid: an open database of COVID-19 literature, a curated literature hub, to track up-to-date scientific information in PubMed (online)
  • HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine (online)
  • Genome Variation Map: a worldwide collection of genome variations across multiple species. Three coronaviruses (SARS-CoV-2, SARS-CoV and MERS-CoV) are for example analyzed. Genomic variants publicly available for the global research community through 2019nCoVR (COVID-19) (online)
  • CovalentInDB: a comprehensive database facilitating the discovery of covalent inhibitors (online)
  • HPO: The Human Phenotype Ontology in 2021 (online)
  • PROTAC-DB: an online database of PROTACs (online)
  • DeepPROTACs: deep learning-based targeted degradation predictor for PROTACs (online)
  • DeepPROTACs: deep learning-based targeted degradation predictor for PROTACs (standalone)
  • DKK: The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases (online)
  • KinaseMD: kinase mutations and drug response database (online)
  • DrugRepV: a compendium of repurposed drugs and chemicals targeting epidemic and pandemic viruses (COVID-19) (online)
  • FOCUS-DB: Food-Additive-Consumption-Safety Database (online)
  • Shennong project: Interactive in silico drug discovery database for SARS-CoV-2 (Covid-19) - Systemic In Silico Screening in Drug Discovery for Coronavirus Disease (COVID-19) with an Online Interactive Web Server (online)
  • HybridMolDB: A Manually Curated Database Dedicated to Hybrid Molecules for Chemical Biology and Drug Discovery (online)
  • NCATS COVID-19: high throughput screening data from the NCATS COVID-19 portal (online)
  • NCATS: include testing of therapeutics against different SARS-CoV-2 variants (Covid-19) (datasets)
  • covid19dataportal: The European Bioinformatics Institute: empowering cooperation in response to a global health crisis (COVID-19 data) (online)
  • Neo4COVID-19: Network pharmacology to defeat Covid-19 (online)
  • R-BIND: RNA-targeted BIoactive ligaNd Database (online)
  • ACD: Antimicrobial Chemotherapeutics Database (online)
  • ScrubChem: a digital curation of PubChem Bioassay (694 million bioactivities, 9,000 molecular targets, 2.3 million chemicals in 2020), designed to build datasets and enhance research (online)
  • KLIFS: Kinase-Ligand Interaction Fingerprints and Structures database is a database that revolves around the protein structure of catalytic kinase domains and the way kinase inhibitors can interact with them (online database)
  • CORAL: Clear and customizable visualization of human kinome data (Kinase) (online)
  • KinMap: a web-based tool for interactive navigation through human kinome data (kinase) (online)
  • ProfKin: A Comprehensive Web Server for Structure-based Kinase Selectivity Profiling (online)
  • KinBase: kinase (online)
  • ASD: a comprehensive database of allosteric proteins and modulators (online)
  • GDSC: Genomics of Drug Sensitivity in Cancer (compounds for cancer - dataset) (online)
  • KLIFS: Kinase database that dissects experimental structures of catalytic kinase domains and the way kinase inhibitors interact with them (online)
  • Kinome Render: look at kinase family (standalone)
  • PathBank: a comprehensive pathway database for model organisms. new, comprehensive, visually rich pathway database containing more than 110 000 machine-readable pathways found in 10 model organisms. Each small molecule is hyperlinked to the rich data contained in public chemical databases such as HMDB or DrugBank and each protein or enzyme complex is hyperlinked to UniProt (online)
  • MeLAD: an integrated resource for metalloenzyme-ligand associations (database online)
  • Kinase Atlas: contains solvent mapping results for all kinases in the Protein Data Bank. You can search this database by PDB ID or by UniProt accession number (online)
  • CCLE: Cancer Cell Line Encyclopedia (online)
  • GUILDify v2.0: A Tool to Identify Molecular Networks Underlying Human Diseases, Their Comorbidities and Their Druggable Targets (online)
  • YaTCM: Yet another Traditional Chinese Medicine Database for Drug Discovery (online)
  • RESPIRE: Repository of Enriched Structures of Proteins Involved in the Red Blood Cell Environment (online database)
  • Kinmap: interactive navigation through human kinome data (online)
  • PKIDB: a Curated, Annotated and Updated Database of Protein Kinase Inhibitors in Clinical Trials (online)
  • BIOFACQUIM: novel compounds databse with natural products isolated and charcterized in Mexico (online)
  • CH/PMUNK: A Virtual Synthesizable Small-Molecule Library for Medicinal Chemistry, Exploitable for Protein-Protein Interaction Modulators (online)
  • nAPOLI: a graph-based strategy to detect and visualize conserved protein-ligand interactions in large-scale (online)
  • The Pathogen Box: contains ~400 diverse, drug-like molecules active against neglected diseases of interest and is available free of charge (ADME-Tox annotated) (online dataset)
  • ALMANAC: The National Cancer Institute ALMANAC: A Comprehensive Screening Resource for the Detection of Anticancer Drug Pairs with Enhanced Therapeutic Activity (online)
  • SAVI: Synthetically Accessible Virtual Inventory (most-synthesizable class comprising 1.09 billion synthetic products) (ultra-large collection) (dataset)
  • GDB-17: 166.4 billion virtual molecules (ultra-large collection) (online)
  • MedPServer: a database for identification of therapeutic targets and novel leads pertaining to natural products (online)
  • ClinicalTrials.gov: registry of clinical trials (online)
  • BitterDB: taste ligands and receptors database (online)
  • V1M: Virtual 1 million macrolide - macrocycles scaffolds (online as suppl file with smiles
  • DrugCombDB: a comprehensive database of drug combinations toward network medicine and combination therapy (database online)
  • DrugComb v2: a more comprehensive drug sensitivity data repository and analysis portal (online)
  • AICD: an integrated anti-inflammatory compounds database for drug discovery (targets and compounds) (online)
  • WebCSD: the on-line portal to the Cambridge Structural Database (CSD), small molecule experimental 3D structures (online)
  • NR-DBIND: Nuclear Receptors Database Including Negative Data
  • Pfam: The Pfam protein families database (online)
  • KinaMetrix: a web resource to investigate kinase conformations and inhibitor space (online)
  • ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms’ proteomes (online)
  • COD: Crystallography Open Database (online)
  • IUPAC: IUPAC Compendium of Chemical Terminology - the Gold Book
  • NextProt: Exploring the universe of human proteins
  • SMMDB: a web-accessible database for small molecule modulators and their targets involved in neurological diseases
  • MobiDB :a database of protein disorder and mobility annotations
  • DrugAge :Database of ageing-related drugs
  • ChemMaps.com: Exploring chemical spaces
  • CircadiOmics: circadian omic web portal
  • DT-Web: DT-Web: a web-based application for drug-target interaction and drug combination prediction through domain-tuned network-based inference (periodically synchronized with DrugBank and PathwayCommons) (online)
  • Therapeutic Target Database (TTD): target and compound data (online)
  • ApoCanD: Database of Human Apoptotic Proteins in the context of cancer
  • Supertarget: an extensive web resource for analyzing 332828 drug-target interactions (displays also pathways, load KEGG, map drugs onto these pathways) (online)
  • GenBank: NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (online)
  • PROSITE: Database of protein domains, families and functional sites (online)
  • SCOP2: Structural Classification of Proteins 2 (online)
  • EMBL-EBI services: many tools for proteins, sequences... (online)
  • OMIM: Online Mendelian Inheritance in Man (online)
  • NPC: the NCGC Pharmaceutical Collection is a comprehensive, publically-accessible collection of approved and investigational drugs
  • KampoDB: database of predicted targets and functional annotations of natural medicines (online)
  • SynPharm: open web resource mainly designed to help synthetic biologists to engineer pharmacological regulation into their proteins (online)
  • NPASS: natural product activity and species source database (online)
  • Super Natural II: a database of natural products (online)
  • HIT: Herbal Ingredients' Targets Database (online)
  • HIT 2.0: an enhanced platform for Herbal Ingredients' Targets (online)
  • VIETHERB: A Database for Vietnamese Herbal Species - Natural products (online)
  • TCM Database@Taiwan: the world's largest traditional Chinese medicine database for drug screening in silico (online)
  • iSMART: an integrated cloud computing web server for traditional Chinese medicine for online virtual screening, de novo evolution and drug design (online)
  • Nubbe: a natural products database from the biodiversity of Brazil (online)
  • COCONUT: the COlleCtion of Open NatUral producTs (dataset)
  • LOTUS: Natural Products Online
  • MCULE: Commercial compound collection (online)
  • COCONUT online: Collection of Open Natural Products database (online)
  • IMPPAT: Indian medicinal plants, ayurvedic medicine (database online)
  • ETM-DB: integrated Ethiopian traditional herbal medicine and phytochemicals database (online)
  • COCONUT: Compound Combination-Oriented Natural Product Database with Unified Terminology (COCONUT) contains traditional medicine, combination drug, functional food, and up-to-date molecular drug/target information from heterogeneous sources, providing valuable resources for polypharmacology studies (online)
  • SANCDB: a South African natural compound database (online)
  • Nanpdb: Northern African Natural Products Database (online)
  • NPACT: naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database (online)
  • The Reactome Pathway Knowledgebase: provides molecular details of signal transduction, transport, DNA replication, metabolism, and other cellular processes as an ordered network of molecular transformations
  • DTC: Drug Target Commons (DTC) is a crowd-sourcing platform to improve the consensus and use of drug-target interactions
  • cBinderDB :a covalent binding agent database
  • Drugs-in-3D: Drug and Drug Target Mapping at the PDB
  • DiPPI: A curated dataset for drug-like molecules in protein-protein interfaces (data online)
  • 2P2I: Protein-Protein Complexes and their Inhibitors (2P2I database) (online)
  • TIMBAL: Protein-Protein interaction inhibitors (online)
  • iPPI-DB: Protein-Protein interaction inhibitors (online)
  • DLiP: Database of Chemical Library for Protein-Protein Interaction (online)
  • iPPI-DB 2021: novel 2021 version of the iPPI-DB, protein-protein interaction inhibitors (online)
  • MOSAIC :a chemical-genetic interaction data repository and web resource for exploring chemical modes of action
  • ProteomicsDB :Human proteins, peptides, inhibitors and analytics
  • FooDB :large resource on food constituents, chemistry and biology
  • AdditiveChem: A comprehensive bioinformatics knowledge-base for food additive chemicals (about 9000) (online)
  • NutriChem 2.0 :exploring the effect of plant-based foods on human health and drug efficacy (natural product)
  • ChemAgora Portal :Searching Online Chemical Data Repositories
  • jMorp :Japanese Multi Omics Reference Panel (database containing metabolome and proteome data for plasma obtained from >5000 healthy volunteers)
  • THPdb :Database of FDA-approved peptide and protein therapeutics
  • DrugPort :Approved drugs in complex with targets (X-ray structures)
  • dbPTM :Protein post-translational modifications (PTMs) database
  • CATH-Gene3D: Gene3D uses the information in CATH to predict the locations of structural domains on millions of protein sequences available in public databases (Protein domain visualisation in gene trees, Domain architecture pages, multiple sequence alignments mapped in 3D, etc) (online)
  • CATH: classification of protein structures downloaded from the Protein Data Bank (online)
  • WikiPathways :a multifaceted pathway database bridging metabolomics to other omics research (can be seen in Cytoscape) (online)
  • pathDIP: an extended pathway annotations and enrichment analysis resource for human, model organisms and domesticated species(integrates 24 major databases) (online)
  • KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold. Helps linking genes to KEGG resources such as the KEGG pathway maps and facilitates molecular network reconstruction (online)
  • PathVisio: free open-source biological pathway analysis software that allows you to draw, edit and analyze biological pathways (standalone)
  • Pathway Commons: Access and discover data integrated from public pathway and interactions databases (online)
  • Target-Pathogen :a structural bioinformatic approach to prioritize drug targets in pathogens
  • FlavorDB :repository of flavor molecules, their natural sources, physicochemical properties, and sensory responses (about 25,595 flavor molecules)
  • PharmacoDB :Mine multiple cancer pharmacogenomic datasets (to find where a drug or cell line of interest has been profiled, and to view and compare the dose-response data for a specific cell line - drug pair)
  • DISNOR : 3700 disease-pathways, mutations, protein-disease association data..etc
  • HPP :Human Proteome Project (HPP and HUPO)
  • Protein Data Bank Japan (PDBj) (many tools including Molmil, ProMode-Elastic server, Omokage search for molecular shape similarity)
  • Protein Data Bank Europe (PDBe) (many tools)
  • PDBminer: Find and Annotate Protein Structures for Computational Analysis (standalone)
  • Prot2HG: a database of protein domains mapped to the human genome (online)
  • Drug To PDB IDs Mappings: database (online)
  • Protein Data Bank RCSB PDB: many tools and search utilities (special pages on Covid-19, online)
  • PDB-Dev: prototype archiving system for structural models in 3D obtained using integrative or hybrid modeling (online)
  • ValTrendsDB: bringing Protein Data Bank validation information closer to the user (online)
  • PDB-Dev (a Prototype System for Depositing Integrative/Hybrid Structural Models)
  • UniProt (many tools including genes' ID converter, SNPs, ...)
  • Ensembl (research on vertebrate genomes, SNPs...)
  • MalaCards (human diseases)
  • InterPro (classify protein sequences into families and domains)
  • CDD/SPARCLE (functional classification of proteins, domains)
  • DrugBank: medicinal drugs, experimental drugs...
  • DrugCentral: medicinal drugs
  • DGIdb 5.0 rebuilding the drug-gene interaction database for precision medicine and drug discovery platforms
  • WITHDRAWN: withdrawn and discontinued drugs
  • ECOdrug a database connecting drugs and conservation of their targets across species
  • SuperDRUG2: a one stop resource for approved/marketed drugs
  • e-Drug3d: offers a facility to explore FDA approved drugs and active metabolites
  • SISTEMAT: is suite of tools to manage databank of secondary metabolites (online)
  • Chembl: annotated compounds, medicinal drugs...
  • CIIPro: a new read-across portal to fill data gaps using public large-scale chemical and biological data (automatically extract in vitro biological data from public resources (i.e. PubChem) for user-supplied compounds) (standalone)
  • PubChem: molecules tested via HTS and more
  • Fetch PubChem compounds
  • Fetch PubChem compounds with Ligdig
  • Chebi: Chemical Entities of Biological Interest
  • KEGG ligand: contains our knowledge on the universe of chemical substances and reactions that are relevant to life
  • PDBeChem: Chemical Components in the PDB
  • HEDD the human epigenetic drug database
  • NPC Pharmaceutical Collection
  • ZINC20 A Free Ultralarge-Scale Chemical Database for Ligand Discovery (online)
  • Zinc: a free database of commercially-available compounds
  • ZINC Express: A Virtual Assistant for Purchasing Compounds Annotated in the ZINC Database (online)
  • Molport: commercially-available compounds
  • eMolecules: commercially-available compounds
  • ChemSpider: commercially-available compounds
  • BioLiP: a semi-manually curated database for high-quality, biologically relevant ligand-protein binding interactions
  • TTD: Therapeutic Target Database
  • SWEETLEAD: An in silico database of approved drugs, regulated chemicals, and herbal isolates
  • DCDB: drug combination database
  • SuperTarget: an extensive web resource for analyzing 332828 drug-target interactions
  • Matador: Manually Annotated Targets and Drugs Online Resource
  • PLIC
  • PoSSuM(pocket comparison online)
  • ProBis: pocket comparison online
  • sc-PDB: An Annotated Database of Druggable Binding Sites from the Protein DataBank
  • PDB: protein databank
  • PDBe: protein databank europe
  • Credo: A Structural Interactomics Database For Drug Discovery
  • PDBbind: comprehensive collection of the experimentally measured binding affinity data for all types of biomolecular complexes deposited in the Protein Data Bank (PDB)
  • PLI: PROTEIN-LIGAND Interaction is a database that describes the interactions that a small molecules (identified by a Het_Id code) perform with target proteins, as observed in PDB complexes
  • FDALabel: drugs Online Label Repository
  • FDA Novel Drug Approvals (2021): a COVID-19 resource compendium (online)
  • Binding DB
  • Wikipedia chemical structure explorer: online tool to explore chemicals from Wikipedia
  • BioGRID: curated set of data have been updated to include interactions, chemical associations, and post-translational modifications (PTM) from many publications
  • SBKB: Structural Biology Knowledgebase
  • Pharos (druggable genome)
  • OpenTargets platform: Find new targets for drug discovery
  • TargeteMine: A new vision into drug target analysis (online)
  • TargetDB: querry multiple publicly available databases and provide an integrated view of the information available about potential targets (standalone)
  • DPD: Dark Proteome Database (online)
  • Binding MOAD: a subset of the Protein Data Bank (PDB), containing every high-quality example of ligand-protein binding
  • OpenTargets: A partnership to transform drug discovery through the systematic identification and prioritisation of targets
  • DGIdb: Drug gene interactions database
  • Pharos druggable genome - TCRD
  • DTO drug target ontology
  • Pharos Pubmed Score PMScore
  • 3did: database of three-dimensional interacting domains (3did)
  • PharmGKB: Pharmacogenomics, variants...
  • Collection of drugs Illuminating the druggable genome
  • The IUPHAR/BPS Guide to PHARMACOLOGY
  • Harmonizome: Integrated knowledge about genes and proteins
  • MolData: a molecular benchmark for disease and target based machine learning (database)
  • Psychoactive Drug Screening Program Ki database: dataset (database)
  • Papyrus: a large-scale curated dataset aimed at bioactivity predictions (database)
  • CARA: Benchmarking compound activity prediction for real-world drug discovery applications (standalone)
  • ExCAPE-DB chemogenomics database (online)
  • ExCAPE-DB chemogenomics database (datasets)
  • Papyrus: a large-scale curated dataset aimed at bioactivity predictions (data online)
  • MBC and ECBL Libraries: outstanding compound collection tools for drug discovery (standalone)
  • bioactivity_dataset: A consensus bioactivity dataset for data-driven drug design and chemogenomics (dataset)
  • FastTargetPred-Chembl29-dataset: A new ChEMBL dataset for FastTargetPred and target fishing for an exhaustive list of linear tetrapeptides (chemogenomics) (dataset)
  • Chemical Probes: Chemical Probes Portal is designed to change the way scientists find and use small-molecule reagents called chemical probes in biomedical research and drug discovery
  • Consensuspathdb: integrates interaction networks in Homo sapiens including binary and complex protein-protein, genetic, metabolic, signaling, gene regulatory and drug-target interactions, as well as biochemical pathways
  • Pathguide: Pathguide contains information about 702 biological pathway related resources and molecular interaction related resources
  • Cancer Cell Map Initiative (CCMI)
  • DTome: Drug-Target Interactome
  • NPCARE: database of natural products (cancer)
  • LOINC (common language clinical and laboratory)
  • Chemical Identifier Resolver (CIR)
  • Aggregate Analysis of ClincalTrials.gov (AACT)
  • The Small Molecule Pathway Database (SMPDB)
  • Fragment Database FDB-17 (10 million)
  • TargetMine (tools for target prioritization)
  • InfoRNA (ligands for RNA)
  • UniChem (cross-references between chemical structure identifiers from different databases)
  • Minepath.org (interactive pathway analysis)
  • XTalkDB: a database of signaling pathway crosstalk
  • Drugs.com :data about drugs and clinical trials (check also drugs.com for drug-drug interactions, DDI), online
  • SMMRNA: a database of small molecule modulators of RNA
  • DrugKiNET (kinase inhibitors)
  • Nucleic acid ligand database (NALDB)
  • Probes & Drugs portal: a public resource joining together focused libraries of bioactive compounds (probes, drugs, specific inhibitor sets etc.) with commercially available screening libraries. The purpose of the portal is to reflect the current state of bioactive compound space and to enable its exploration from different points of view

Repositioning, repurposing,
polypharmacology, target fishing, drug combination

  • Chemogenomic-Model: In-Silico Target Prediction by Ensemble Chemogenomic Model based on Multi-Scale Information of Chemical Structures and Protein Sequences (standalone)
  • MOViDA: multiomics visible drug activity prediction with a biologically informed neural network model (DTI) (standalone)
  • DTINet: A Network Integration Approach for Drug-Target Interaction Prediction (standalone)
  • DACPGTN: An end-to-end model DACPGTN for predicting ATC code for a given drug (standalone)
  • CDCDB: Continuous-Drug Combination DataBase (online)
  • DrugRepo: a novel approach to repurposing drugs based on chemical and genomic features (online)
  • DrugRep: an automatic virtual screening server (structure-based or ligand-based) for drug repurposing (online)
  • EviCor: Interactive Web Platform for Exploration of Molecular Features and Response to Anti-cancer Drugs (online)
  • PLATO: Polypharmacology pLATform predictiOn (target fishing) (online)
  • PharmOmics: A species- and tissue-specific drug signature database and gene-network-based drug repositioning tool (online)
  • DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules (text mining) (appyters) (online)
  • DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules (text mining) (online)
  • SBGNview: towards data analysis, integration and visualization on all pathways (standalone)
  • PATHOME-Drug: a subpathway-based polypharmacology drug-repositioning method (online)
  • cov_target: COV-Drug Target interaction server for Covid-19 Drug Repurposing (online)
  • DRUIDom: Protein domain-based prediction of drug/compound-target interactions (DRUg Interacting Domain prediction, DTI) - (PubChem - Chembl datasets) (standalone)
  • Multiscale-interactome: Identification of disease treatment mechanisms through the multiscale interactome (standalone)
  • CSNAP3D: 3D chemical similarity using a network algorithms score - target fishing (online)
  • STarFish: combining multiple multi-target QSAR models for target fishing (model stacking) - target fishing (standalone)
  • drugtargets: Discovering protein drug targets using knowledge graph embeddings (online)
  • EMuSSel: Quantitative Polypharmacology Profiling Based on a Multifingerprint Similarity Predictive Approach (online)
  • DGB: Drug Gene Budger Assists investigators in order to prioritize small molecules that are predicted to maximally influence the expression of their target gene of interest. Users can enter a gene symbol along with the wish to upregulate or downregulate its expression. Data signatures are extracted from the LINCS L1000 dataset, the original Connectivity Map (CMap) dataset, and the Gene Expression Omnibus (GEO) (online)
  • CREEDS: Crowd Extracted Expression of Differential Signatures (online database)
  • DrugMatrix: Molecular toxicology reference database and informatics system. Large-scale gene expression data (online database)
  • CEBS: Chemical Effects in Biological Systems (online database)
  • VirtualFlow @ Covid19: Ultra-large structure-based virtual screening SARS-CoV-2 related targets (top 1 million compounds and repositioning) (COVID-19 datasets online)
  • LigAdvisor: a versatile and user-friendly web-platformfor drug design (online)
  • CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations (standalone and online)
  • ePharmaLib: A Versatile Library of e-Pharmacophores to Address Small-Molecule (Poly-)Pharmacology. A library of 15,148 e-pharmacophores modeled from solved structures of pharmaceutically relevant protein-ligand complexes of the screening Protein Data Bank (sc-PDB). ePharmaLib can be used for target fishing of phenotypic hits, side effect predictions, drug repurposing, and scaffold hopping (online)
  • NOD: a server to predict New use of Old Drugs to facilitate drug repurposing. The query starts by a list of targets of potential interest (online)
  • PharmOmics: prediction of potential drugs targeting disease processes that were identified by Mergeomics (online)
  • Standardize Drug Names: script to standardize drug names (standalone)
  • LigTMap: ligand and structure-based target identification and activity prediction for small molecular compounds (online)
  • LigTMap: ligand and structure-based target identification and activity prediction for small molecular compounds (standalone)
  • multi_DTI: Deep learning integration of molecular and interactome data for protein–compound interaction prediction (standalone)
  • PHENSIM: RapidIdentification of Druggable Targets and the Power of the PHENotype SIMulator for Effective Drug Repurposing in COVID-19 (online)
  • PHENSIM: RapidIdentification of Druggable Targets and the Power of the PHENotype SIMulator for Effective Drug Repurposing in COVID-19 (standalone)
  • LigTMap: Ligand and Structure-Based Target Identification and Activity Prediction for Small Molecular Compounds (identify protein targets of chemical compounds among 17 classes of therapeutic proteins (and 6000+ proteins) (profiling) (online)
  • Epigenetic Target Profiler: A Web Server to Predict Epigenetic Targets of Small Molecules (online)
  • FRAGSITE: A Fragment-Based Approach for Virtual Ligand Screening. For virtual ligand screening: screening a protein against library of compounds. For virtual target screening: screening a compound against the Human proteome (online)
  • CCVPAP-SARS-COV-2: A Modelling Framework for Embedding-based Predictions for Compound-Viral Protein Activity (Covid-19) (standalone)
  • ReFRAME: collection of 12,000 compounds is a best-in-class drug repurposing library containing nearly all small molecules that have reached clinical development or undergone significant preclinical profiling (online)
  • Drugvirus.info: Broad-spectrum antiviral agents (BSAAs) and viruses they inhibit (Covid-19) (online)
  • PROMISCUOUS 2.0: a resource for drug-repositioning. Contains four different types of entities: Drugs, Proteins, side-effects and indications including relations between them for a global view, data for COVID-19 (online)
  • DrugRepV: a compendium of repurposed drugs and chemicals targeting epidemic and pandemic viruses (COVID-19) (online)
  • DRDOCK: performs online automatic virtual drug screening of 2016 FDA-approved drugs on a user-submitted target protein. Combines molecular docking and molecular dynamic simulations to prioritize strong binders from less likely binders (online)
  • CORDITE: CORona Drug InTERactions database - COVID-19 (database online)
  • The COVID19 Drug Repository server: text-mining the literature in search of putative COVID19 therapeutics (COVID-19) (online)
  • CoronaVIR: predicted and existing information on coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (COVID-19) (online)
  • H-RACS: a handy tool to rank anti-cancer synergistic drugs (online)
  • DockThor-VS Web Server: Virtual Screening focusing on SARS-CoV-2 Therapeutic Targets and their Non-Synonym Variants (Covid-19), drug Repurposing (online)
  • DrugSpaceX: a large screenable and synthetically tractable database extending the approved drug space (online)
  • DockCoV2: a drug database against SARS-CoV-2 (COVID-19) (online)
  • CAS COVID-19 antiviral candidate compounds: 50000 compounds (dataset)
  • PubChem COVID-19: COVID-19 (Coronavirus Disease 2019) data in PubChem (data)
  • DrugBank COVID-19: COVID-19 (Coronavirus Disease 2019) data in PubChem (data)
  • ChEMBL_27 SARS-CoV-2 release: COVID-19 experimental screening (dataset)
  • SPVec: Codes and datasets for SPVec, A Word2vec-inspired feature representation method for Drug-Target Interaction Prediction (standalone)
  • CaNDis: investigation of causal relationships between diseases, drugs, and drug targets. Can be used to identify candidate genes with known and novel roles in disease co-occurrence and drug-drug interactions (online)
  • COVID-19: COVID-19 Worldwide Preclinical Studies, Targeting COVID-19 Portal (dataset online)
  • Virus-CKB: an integrated (small molecules, mAb, targets...) bioinformatics platform and analysis resource for COVID-19 research (online)
  • Wiki-CORONA: Search for PPIs related to Coronavirus Infection (COVID-19) (online)
  • Chemical Checker Covid-19: Bioactivity Profile Similarities to Expand the Repertoire of COVID-19 Drugs, suggested compounds and possible targets (dataset)
  • Stanford Coronavirus Antiviral Research Database: compounds and some possible targets COVID-19 Drugs (dataset)
  • MTiOpenScreen (repositioning): Online structure-based screening of purchasable approved drugs and natural compounds: retrospective examples of drug repositioning on cancer targets - (used for COVID-19, the Drugs-lib is used, the reference is Lagarde et al., PMID: 30190791) (online)
  • FastTargetPred: a program enabling the fast prediction of putative protein targets for input chemical databases - drug repositioning, phenotypic screening... drug target interactions... (standalone)
  • ADRriskestimator: The Development of a Scoring and Ranking Strategy for a Patient-Tailored Adverse Drug Reaction Prediction in Polypharmacy (drug combination, toxicity) (online)
  • HDR: Drug repositioning based on a heterogeneous network of drugs and diseases (Cytoscape standalone app)
  • DrugSimDB: a comprehensive database of multi-modal drug similarity measures by integrating variety of heterogenous datasets available online. Current version of DrugSimDB includes chemical, structure, pathway, and functional GO terms similarities of 10,317 small-molecule drugs, yielding 238,635 drug-pairs with significant aggregated score (online)
  • IntelliPatent: a web-based intelligent system for fast chemical patent claim drafting (hit2lead...) (online)
  • Chemical Checker on Covid19: Expanding the universe of drugs to fight SARS-CoV-2 (Covid19) (online)
  • MDock: automated molecular docking software to simultaneously dock ligands against multiple protein structures or conformations by using the ensemble docking algorithm (standalone)
  • cando.py: Open Source Software for Predictive Bioanalytics of Large Scale Drug-Protein-Disease Data (Conda Python package installer, standalone)
  • iBioProVis: Interactive Visualization and Analysis of Compound Bioactivity Space (drug repositioning - target fishing - online)
  • NPCPD2: Phenotypic Drug Discovery Resource, about 2,500 clinically approved compounds screened in 35 phenotypic assays (dataset)
  • CTRP: the Cancer Therapeutic Response Portal measured sensitivity of 242 genetically characterized cancer cell lines to 354 small molecule probes and drugs (dataset)
  • CCLE: The Cancer Cell Line Encyclopedia (dataset)
  • CC: Chemical Checker provides processed, harmonized and integrated bioactivity data on about 800,000 small molecules (combined similarity search and biological activity named CC signatures). The tool helps for target identification and library characterization, discovery of compounds that reverse and mimic biological signatures of disease models and genetic perturbations (online)
  • GalaxySagittarius: Structure- And Similarity-Based Prediction of Protein Targets for Drug-Like Compounds (input 1 ligand) - Target Fishing (online)
  • PaccMann: A Web Service for Interpretable Anticancer Compound Sensitivity Prediction (drug repositioning - online)
  • QuartataWeb: Chemical-protein-pathway mapping for polypharmacology and chemogenomics. (Users can easily obtain information on experimentally verified (known) and computationally predicted (new) interactions between 5,494 drugs and 2,807 human proteins in DrugBank, and between 315,514 chemicals and 9,457 human proteins in the STITCH database). Query a series of chemicals, drug combinations, or multiple targets, to enable multi-drug, multi-target, multi-pathway analyses (online)
  • iATC-FRAKEL: A simple multi-label web-server for recognizing anatomical therapeutic chemical classes of drugs with their fingerprints only (ATC code) (online)
  • iATC-NRAKEL: An Efficient Multi-Label Classifier for Recognizing Anatomical Therapeutic Chemical Classes of Drugs (standalone)
  • ATC code prediction: Anatomical Therapeutic Chemical Classes of Drugs (standalone)
  • iDTI-ESBoost: Identification of Drug Target Interaction Using Evolutionary and Structural Features with Boosting (DTI) (online)
  • Polypharmacology: A Python implementation of Polypharmacology pipeline to generate a dataset of reference ligands, perform in silico target fishing on the dataset, identify similar compounds between two or more targets in the dataset etc. (standalone)
  • SmartGraph: a network pharmacology investigation platform (performs bioactivity predictions) (online)
  • DrugClust: A machine learning approach for drugs side effects prediction (R, standalone)
  • Genomics of Drug Sensitivity in Cancer (GDSC): data set contains over 1000 cancer cell lines and 225 drugs (database online)
  • iATC-NRAKEL: an efficient multi-label classifier for recognizing anatomical therapeutic chemical classes of drugs (ATC) (standalone)
  • eModel-BDB: database of comparative structure models of drug-target interactions from the Binding Database (database online)
  • MPDSDM: Molecular Property Diagnostic Suite - Diabetes Mellitus (MPDSDM) is a Galaxy-based, open source disease-specific web portal for diabetes. It consists of three modules namely (i) data library (ii) data processing and (iii) data analysis tools (online)
  • PharmacoGx: an R package for analysis of large pharmacogenomic datasets (gene signature) (standalone)
  • ACID: a free tool for drug repurposing using consensus inverse docking strategy (online)
  • Drug-Class: Learning Drug Functions from Chemical Structures with Convolutional Neural Networks and Random Forests (standalone)
  • Centerwatch: Prescription drugs and drugs approved by the FDA by year - Database (online)
  • DIA-DB: prediction of diabetes drugs (ligand-based and inverse screening) (online)
  • DailyMed: provides trustworthy information about marketed drugs in the United States - Database (online)
  • DeepScreening: a deep learning-based screening web server for accelerating drug discovery (online)
  • DRUDIT: Web-Based DRUgs DIscovery Tools to Design Small Molecules as Modulators of Biological Targets, Multi-Target and On/Off-Target tasks (online, need password)
  • LSC: Large-scale comparison of machine learning methods for drug target prediction on ChEMBL (code and datasets, deeplearning... standalone)
  • MuSSel: Multi-fingerprint Similarity Search aLgorithm, tool to find putative protein drug targets of small molecules or to repurpose (reposition) existing bioactive compounds. Target fishing, polypharmacology (online)
  • CancerDrugMap: Extended Multitarget Pharmacology of Anticancer Drugs (online)
  • X2K: Web infers upstream regulatory networks from signatures of differentially expressed genes (standalone)
  • DeepCOP: deep learning-based approach to predict gene regulating effects of small molecules (standalone)
  • deepDR: A network-based deep learning approach to in silico drug repositioning (standalone)
  • DrugZ: DrugZ is an open-source Python software for the analysis of genome-scale drug modifier screens. The software accurately identifies genetic perturbations that enhance or suppress drug activity. Identifying chemogenetic interactions from CRISPR screens with drugZ (standalone)
  • CRDS: Consensus Reverse Docking System for Target Fishing (reverse docking against 5254 target proteins for one given ligand ID from PubChem or ZINC) (online)
  • EK-DRD: A Comprehensive Database for Drug Repositioning Inspired by Experimental Knowledge. EK-DRD contains experimentally validated drug repositioning annotation for 1861 FDA-approved and 102 withdrawn small molecule drugs. Annotation is done at four levels, using 30,944 target assay records, 3999 cell assay records, 585 organism assay records, and 8910 clinical trial records (online)
  • ReactomeFIViz: drug-target visualization in the context of pathways and networks (integrates drug-target interaction information with high quality manually curated pathways and a genome-wide human functional interaction network). Both the pathways and the functional interaction network are provided by Reactome (Reactome Cytoscape app standalone)
  • Bioactivity-explorer: a web application for interactive visualization and exploration of bioactivity data (from ChEMBL, network, disease…) (online and standalone)
  • PPB2: Polypharmacology prediction (online)
  • PROTEINATOR: enables repurposing of leads based on secondary interactions. Direct Drugs are listed and Indirect Drugs (Compounds that bind to the 'first-neighbour' of the primary protein(s)) (online)
  • PatchSearch: a web server for off-target protein identification (input a protein complexed with a ligand and identifies within user-defined or predefined collections of protein structures, those having a binding site compatible with this ligand in terms of geometry and physicochemical properties) (online)
  • Drug ReposER: web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning (pocket comparison, ligand transposition) (online)
  • CSgator: an integrated web platform for compound set analysis, can be used for toxicity and investigate polypharmacology (online)
  • DrugComb: an integrative cancer drug combination data portal (online)
  • MolTarPred: a web tool for comprehensive target prediction with reliability estimation (online)
  • DEEPScreen: Virtual Screening Using Convolutional Neural Networks By Images of Compounds (standalone)
  • TIN-X: target importance and novelty explorer (prediction via text mining) (online)
  • DrugR+: database for drug repurposing, combination therapy, and replacement therapy (online)
  • ReDO_DB: the repurposing drugs in oncology database (online)
  • Target2: Predicting protein targets for drug-like compounds using transcriptomics (LINCS Data) (data set)
  • Drug Targetor: a web interface to investigate the human druggome for over 500 phenotypes
  • PathwayMap: Fast prediction of the interaction between a set of ligands (similarity) and major human biological and signaling pathways using state-of-the-art neural networks (online)
  • DTP: Interactive visual analysis of drug–target interaction networks using Drug Target Profiler, with applications to precision medicine and drug repurposing (online)
  • CONNECTOR: predicts propensity of putative drug-protein interactions based on similarity between the input drug structure, drug profile, and/or protein sequence and the experimental drug-protein interactions that are included in the internal database (online)
  • DIGREM: Drug-Induced Genomic Response models for identification of Effective Multi-drug combinations, an online tool kit that can effectively predict drug synergy (online)
  • HitPickV2: a Web Server to predict targets of chemical compounds (polypharmacology, profiling), input smiles (online)
  • Drug-Target Explorer: DTexplorer, Probing the chemical–biological relationship space (phenotypic screening, polypharmacology, prediction of molecular targets for novel molecules based on structural similarity (online)
  • PharmacoDB: Mine multiple cancer pharmacogenomic datasets (to find where a drug or cell line of interest has been profiled, and to view and compare the dose-response data for a specific cell line - drug pair) (online)
  • SynergyFinder: a web application for analyzing drug combination dose-response matrix data (online)
  • SynergyFinder: an interactive tool for analyzing drug combination dose-response data (online)
  • SYNERGxDB: an integrative pharmacogenomic portal to identify synergistic drug combinations for precision oncology (online)
  • CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets (online)
  • Combenefit: an interactive platform for the analysis and visualization of drug combinations (for windows) standalone
  • DRRS: Computational drug repositioning using low-rank matrix approximation and randomized algorithms (standalone)
  • ChemMapper: a versatile web server for exploring pharmacology and chemical structure association based on molecular 3D similarity method (online, still running?)
  • ChemProt 3: a ressource of annotated and predicted chemical-protein interactions (input can be SMILES, online)
  • Similarity ensemble approach (SEA): the approach relates proteins based on the set-wise chemical similarity among their ligands (online)
  • Open Targets: visualisation of potential drug targets associated with disease (online)
  • DrugDiseaseNet: a novel computational approach for drug repurposing using systems biology (R package) (standalone)
  • eRepo-ORP: contains data generated for the repositioning of DrugBank drugs to Orphanet proteins (online data)
  • RFQSAR: random Forest QSAR models for target identification and fishing (target deconvolution in phenotypic screening, polypharmacology, repositioning), 1121 human targets were built by random forest algorithm using bioactivity data from ChEMBL (input smiles, online)
  • Chemotext: Publicly-Available Web Server for Mining Drug-Target-Disease Relationships in PubMed (polypharmacology, repositioning...) (online)
  • TargetNet: a web service for predicting potential drug-target interaction profiling via multi-target SAR models. When the user submits a molecule, the server will predict the activity of the user’s molecule across 623 human proteins by establishing the high quality QSAR model for each human protein (thus 623 QSAR models), thus generating a DTI profiling that can used as a feature vector for wide applications (online)
  • Probe Miner: Objective Assessment of Chemical Probes. This resource provides evaluation of > 1.8m small molecules against for >2,200 human targets (online, input target name)
  • PhID: Integrated Pharmacology Interactions Database for Drugs, Targets, Diseases, Genes, Side-Effects, and Pathways (visualize, online)
  • DTINet: novel drug–target interactions from a constructed heterogeneous network (standalone)
  • STOPGAP: Systematic Target OPportunity assessment by Genetic Association Predictions (online)
  • ChemViz2: extends the capabilities of Cytoscape into the domain of cheminformatics (Cytoscape App, standalone, help to visualize data)
  • DRAR-CPI: This server has a representative collection of drug molecules and targetable human proteins. When you submit a molecule, the server will suggest candidate off-targets that tend to interact with it, and will also give the positive or negative association scores between your molecule and our library drugs based on their interaction profiles of the CPI. Since our library drugs have annotations of their indications and ADRs, you can thus predict new indications or unknown ADRs based on the association scores of your molecule across our library molecules (need registration, online)
  • AVCpred: Antiviral compound prediction via QSAR (input SDF, online)
  • HitPick: web server that facilitates the analysis of chemical screenings by identifying hits and predicting their molecular targets. The target prediction functionality can also be used in a stand-alone fashion (online and standalone, input smiles)
  • idTarget: A web server for identifying biomolecular targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach (online)
  • SPiDER: self-organizing map–based prediction of drug equivalence relationships (online)
  • Mantra: computational tool for the analysis of the Mode of Action (MoA) of novel drugs and the identification of known and approved candidates for “drug repositioning”. It is based on network theory and non-parametric statistics on gene expression data (online)
  • PASS: predicts over 4000 kinds of biological activity, including pharmacological effects, mechanisms of action, toxic and adverse effects, interaction with metabolic enzymes and transporters, influence on gene expression, etc (online)
  • SwissTargetPrediction: allows to predict the targets of a small molecule. Using a combination of 2D and 3D similarity measures, it compares the query molecule to a library of 280'000 compounds active on more than 2000 targets of 5 different organisms (online)
  • SuperPred: a prediction webserver for ATC code and target predicition of compounds (online)
  • TargetHunter
  • TarFisDock: the Targets Associated with its MOst SImilar Counterparts, by exploring the largest chemogenomical databases (online)
  • DGIdb 4: Drug gene interactions database. User-friendly browsing, searching, and filtering of information on drug-gene interactions and the druggable genome, mined from over thirty trusted sources (online)
  • FDALabel: Online Label Repository (online)
  • KEGG Drug: comprehensive drug information resource for approved drugs in Japan, USA, and Europe (online)
  • Supertarget: an extensive web resource for analyzing 332828 drug-target interactions (online)
  • MATADOR: Manually Annotated Targets and Drugs Online Resource (online)
  • DrugCentral: search by drug, target name and by pharmacologic action (online)
  • CRIBdb NME: contains useful information regarding NMEs - approved drugs (database online)
  • ChemCom: (Chemical Comparator) is a computer application which facilitates searching and comparing chemical libraries (standalone)
  • DRUGSURV: a resource for repositioning of approved and experimental drugs in oncology based on patient survival information derived from clinical cancer expression datasets (online)
  • DINIES: Drug-target Interaction Network Inference Engine based on Supervised Analysis enables us to predict potential interactions between drug molecules and target proteins, based on drug data and omics-scale protein data (online)
  • BalestraWeb: efficient online evaluation of drug–target interactions (online)
  • LigSearch: Identification of possible ligands from 3D protein structure or sequence (online)
  • systemsDock: web server for network pharmacology-based prediction and analysis, which applies high-precision docking simulation and molecular pathway map to comprehensively characterize the ligand selectivity and to illustrate how a ligand acts on a complex molecular network (online) input 5 small molecules max
  • Ligdig: application for investigating ligand-protein interactions. LigDig can be used to query structural and functional properties, compare binding sites... (online)
  • Drugquest: text mining (online)
  • PLIC: Clusters of similar binding sites in the PDB and analysis of various type of interactions within the clusters (online)
  • PoSSuM: pocket similarity search (online)
  • ProBis: align protein binding site (online)
  • DT-Web: drug target interaction prediction, drug combination (online and standalone, R package)
  • sc-PDB: Annotated Database of Druggable Binding Sites from the Protein DataBank (online)
  • DASPfind: New Efficient Method to Predict Drug-Target Interactions (online)
  • KEGG: Kyoto Encyclopedia of Genes and Genomes (database online)
  • GO: Gene Ontology Consortium (online)
  • UniProt: provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information (online)
  • iGPCR-Drug: Predicting drug-GPCR interaction in cellular networking (input drug code and protein sequence) (online)
  • PDTD: Potential Drug Target Database (online)
  • CancerResource: It is a comprehensive knowledgebase for drug-target relationships related to cancer as well as for supporting information or experimental data (online)
  • Carlsbad: Select either the Targets or Structures tab above to search for targets or structures, respectively (database online)
  • GEO2R: compare two or more groups of Samples in order to identify genes that are differentially expressed across experimental conditions (online)
  • PDID: Protein-Drug Interaction Database in the structural human proteome (similar binding site, docking, inverse docking) (online)
  • iDTP: An integrated structure- and system-based framework to identify new targets of metabolites and known drugs (standalone)
  • iDrug-Target: A package of web-services for predicting drug-target interaction (online)
  • e-LEA3D: docking (online)
  • iDrug: online drug discovery (similarity, pharmacophore..) (online)
  • MANORAA: Mapping Analogous Nuclei Onto Residue And Affinity for identifying protein–ligand fragment interaction, pathways and SNPs (online)
  • DrugTargetInspector: Assistance tool for patient treatment stratification (online)
  • K-Map (KMap, Kinase Map), connecting kinases with therapeutics for drug repurposing and development, input kinase name (online)
  • iATC-mISF (ATC predictor): a multi-label classifier for predicting the classes of anatomical therapeutic chemicals (input smiles, online)
  • iATC-mHyb: hybrid multi-label classier for predicting the classication of anatomical therapeutic chemicals, online
  • Phenolyzer: stands for Phenotype Based Gene Analyzer, a tool focusing on discovering genes based on user-specific disease/phenotype terms (online)
  • Gusar antitargets...developed to create QSAR/QSPR models on the basis of the appropriate training sets represented as SDfile contained data about chemical structures and endpoint in quantitative terms (online, input draw a compound)
  • DRABAL: Novel Method for Mining Large High-throughput Screening Assays using Bayesian Active Learning (standalone)
  • webDrugCS: Interactive 3D-Visualization of DrugBank chemical space in the web browser (online)
  • DTIPRED: Computational Discovery of Putative Leads for Drug Repositioning Through Drug-Target Interaction Prediction (standalone)
  • MeSHDD (text mining) MeSH-based Drug-Drug Similarity and Repositioning (online)
  • MeSHHeading2vec: a new method for representing MeSH headings as vectors based on graph embedding algorithm (standalone)
  • PatchSearch (pocket-based) standalone
  • RepoDB (database for drug repositioning) online
  • SIMCOMP/SUBCOMP (target fishing), input mol file, online
  • CSNAP (target fishing), Large-scale Chemical Similarity Networks for Drug Target Profiling of Compounds Identified in Cell-based Chemical Screens (online)
  • Drug Repurposing Hub (online)
  • RepurposeDB Explore repositioned drug (online)
  • Off-label and polypharmacy side effect databases (online download) (Offsides)
  • Twosides databases (polypharmacy side effects for pairs of drug, online to download)
  • SIDER (ADR of marketed medicines), contains information on marketed medicines and their recorded adverse drug reactions (online)
  • Phenomizer (clinical diagnostics based on genomics and patient symptomology) online
  • LINCSCLOUD or CLUE.IO (perturbation-driven gene expression dataset, online)
  • PRIME (EMA) unmet medical needs (trials), PRIME is a scheme launched by the European Medicines Agency (EMA) to enhance support for the development of medicines that target an unmet medical need
  • PharmMapper (reversed pharmacophore matching, target fishing) online
  • TargetPred Target Prediction: applications for predicting the function of several targets such as proteins in human diseases or molecular proceses by using protein information (Bio-AIMS) online
  • C-SPADE serves as an interactive and innovative visualization tool for drug screening data. It reterives compounds structural information and clusters them based on their structural similarties, which is later visualized as a dendrogram of compounds augmented with their bioactivity values and other compound annotations (Compound SPecific bioActivity DEndrogram, compounds-phenotype) online
  • PPB Polypharmacology Browser, target prediction (online and standalone)
  • Rephetio: Drug repurposing predictions (online)
  • Hetionet (integrative network of biomedicine) standalone
  • NFFinder: bioinformatics approach that combines experimental gene expression profiles and data from publicly available databases to identify conditions or experiments that induce similar or opposite gene expression patterns (conditions that induce similar or opposite gene expression patterns) (online)
  • CoGe (comparative genomics) online
  • Drug Vs Disease An R and Cytoscape plug-in for comparing Drug and Disease profiles (standalone)
  • Enrichr (datasets of diseases, genes..) online, input BED or list of genes
  • Drugs.com (data about drugs and clinical trials) online
  • DrugSig: drug repositioning with gene expression signatures for drug repositioning (online)
  • Drug voyager: exploring unintended drug action
  • JAPIC (side effects) (online)
  • DrugKiNET (kinase inhibitors) online
  • PDSP Ki database
  • Repurposed Drug Database (online)
  • Drug Repurposing Wiki (online)
  • Drug SIGnatures DataBase (DSigDB: Drug Signatures Database for Gene Set Analysis (online)
  • RE:fine Drugs: drug repurposing opportunities (online)
  • Breakthrough Therapies chart: is a list of all publicly announced breakthrough therapy designations since the program’s inception in 2012 (online)
  • SDTNBI: an integrated network and chemoinformatics tool for systematic prediction of drug-target interactions and drug repositioning (standalone)
  • DTome: Drug-Target Interactome (online)
  • PASS Targets predict interactions online (~1534 human proteins) at Way2Drugs
  • chemogenomicAlg4DTIpred: Open-source chemogenomic data-driven algorithms for predicting drug-target interactions (in R) standalone
  • Selenzyme: a free online enzyme selection tool for metabolic pathway design (online)

Data manipulation tools - dataviz - machine learning - descriptors - some datasets - model repository - chemistry toolkit - benchmarking

  • LIT-PCBA: An unbiased dataset for machine learning and virtual screening (standalone)
  • COVID-KOP: Integrating Emerging COVID-19 Data with the ROBOKOP Database (data mining) (online)
  • ugtm: a python package for Generative Topographic Mapping (GTM) - dataviz - classification - regression (standalone)
  • NetSets.js: A JavaScript framework for compositional assessment and comparison of biological networks through Venn integrated Network diagrams (standalone and online)
  • pathDNN: a pathway-guided deep neural network model to predict the drug sensitivity to cancer cells (online)
  • MayaChemTools: similarity search, descriptors, etc, standalone
  • BioShell 3.0: Library for Processing Structural Biology Data (C and Python) (standalone)
  • FPKit: Life beyond the Tanimoto coefcient: similarity measures for interaction fngerprints (Python-based cheminformatics package for fingerprint-related tasks) (standalone)
  • KNIME (eg., HitSEE...), workflow, etc, standalone
  • LillyMol: Eli Lilly set of cheminformatic tools (standalone)
  • ChemmineR: Cheminformatics Toolkit for R, descriptors (standalone)
  • Chempy (descriptors, QSAR, etc)(standalone)
  • RDKit Open-Source Cheminformatics Software, toolkit, ...matched molecular pair, similarity search, etc (on some OS and OS versions very difficult to install...) (standalone)
  • OpenChemLib: Cheminformatics tool kit. Fully Automated Creation of Virtual Chemical Fragment Spaces Using the Open-Source Library OpenChemLib (standalone)
  • MayaChemTools: Cheminformatics tool kit. A growing collection of Perl and Python scripts, modules, and classes to support a variety of day-to-day computational discovery needs (standalone)
  • ErtlFunctionalGroupsFinder: automated rule-based functional group detection with the Chemistry Development Kit (CDK) (standalone)
  • The Caret package for machine learning (standalone)
  • MOLE db: Molecular Descriptors Data Base is a free on-line database comprised of 1124 molecular descriptors calculated for 234773 molecules (online)
  • ClassyFire: web-based application for automated structural classification of chemical entities (online)
  • Entrezpy: A Python library to dynamically interact with the NCBI Entrez databases (standalone)
  • Raincloud plots: a multi-platform tool for robust data visualization (standalone)
  • FuncTree2: an interactive radial tree for functional hierarchies and omics data visualization (online and standalone, eg, via Docker: https://github.com/yamada-lab/functree-ng)
  • iLearn: an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data (e.g., python tools to compute sequence descriptors with several machine learning approaches) (online and standalone)
  • DOGMA: a web server for proteome and transcriptome quality assessment (online and standalone)
  • VisFeature: a stand-alone program for visualizing and analyzing statistical features of biological sequences (standalone)
  • Physicochemical n-Grams Tool: A tool for protein physicochemical descriptor generation Proteomics Data Analysis Tool (standalone - Windows)
  • Dimorphite-DL: an open-source program for enumerating the ionization (protonation) states of drug-like small molecules (standalone, requires RDKIT)
  • PySpark and RDKit: Moving towards Big Data in Cheminformatics (in the supplement of the article) (standalone)
  • Wordclouds: Wordscloud (online)
  • LSTMs: Visual Analysis for Recurrent Neural Networks (machine learning, standalone and online)
  • Tox21: Tox21's 10,000-compound library (Tox21 10K 2014) to build models and look for structure-activity relationships (online datasets)
  • MER: a shell script and annotation server for minimal named entity recognition and linking (Minimal Entity Recognizer, text mining, standalone)
  • LitSense: making sense of biomedical literature at sentence level (text mining, online)
  • OmicsNet: for Network Integration and 3D Visualization including small molecules (online)
  • FigTree: designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures (standalone)
  • Ambit-SMIRKS: a software module for reaction representation, reaction search and structure transformation (standalone)
  • Chemmodlab: A Cheminformatics Modeling Laboratory for Fitting and Assessing Machine Learning Models (standalone)
  • WebGraphviz: is Graphviz (Graphviz is open source graph visualization software) in the Browser (online)
  • Canva: creative graph design (online)
  • Infogram: creative (animated) graphics (online)
  • Faerun: interactive 3D-Visualization of SureChEMBL in the web browser, also available as a Python package (online)
  • Chemmaps: visualize chemical space (online)
  • ChemSAR: full workflow of building a Structure‑Activity/Property Relationship(SAR/SPR) model (online)
  • ChemDes: An integrated web-based platform for molecular descriptor and fingerprint computation (online)
  • Ezqsar: An R Package for Developing QSAR Models Directly From Structures (computes also descriptors…) (standalone)
  • MLViS: machine learning-based virtual screening tool (online)
  • NAViGaTOR: Network Analysis, Visualization, & Graphing TORonto (standalone)
  • D-Tools: online tools for chemistry and data analysis, PUMA (Platform for Unified Molecular Analysis), Activity Landscape Plotter server (ActLSmaps), Consensus Diversity Plots (CDPS) (online)
  • KNIME: Konstanz Information Miner, is a free and open-source data analytics, reporting and integration platform (standalone), toolkit for drug discovery
  • BlueObelisk: Interoperability in Chemical Informatics (standalone), toolkit for drug discovery
  • CDK: toolkit for drug discovery, descriptors (standalone)
  • OpenBabel: toolkit for drug discovery, file format etc (standalone)
  • ODDT: Open Drug Discovery Toolkit, toolkit for drug discovery (standalone)
  • Joelib: Molecular descriptors (standalone)
  • Afgen: Fragment-based descriptors (standalone)
  • DENOPTIM: Software for Computational de Novo Design of Organic and Inorganic Molecules. Virtual compounds. Also utility to fragment small molecules (standalone)
  • ISIDA - fragmentor: Calculate of Substructural Molecular Fragments and ISIDA Fragments (standalone)
  • Web scraping: How to Scrape an HTML website for Chemical Information (python scripts, standalone)
  • Cytoscape: open source software platform for visualizing complex networks and integrating these with any type of attribute data (standalone)
  • Systematic Review toolbox: tools for systematic reviews, text mining (information)
  • Abstract Sifter: a comprehensive front-end system to PubMed (standalone, Microsoft Excel Windows)
  • The Math : Math Online equation solver (online)
  • Databionic ESOM (Emergent Self-Organizing Maps) (standalone)
  • Venny (Venn diagrams to find data in common) (online and standalone)
  • InteractiVenn: a web-based tool for Venn diagrams (up to 6 datasets - online)
  • ChemDB chemoinformatics portal (chemoinformatics tools & datasets) (online)
  • OCHEM (chemoinformatics tools & datasets, model collections) (online)
  • Shinyheatmap for big data genomics (online)
  • QsarDB repository (online)
  • DeepChem Python library democratizing deep learning for science
  • GUSAR@NIH (chemoinformatics tools & datasets) (online)
  • FUn: A Framework for Interactive Visualizations of Large, High Dimensional Datasets on the Web (online)
  • pdb-tools: command line python scripts to manipulate PDB file (standalone)
  • PDB-Tools Web: A user-friendly interface for the manipulation of PDB files (online)
  • Biobox: a toolbox for biomolecular modelling (standalone)
  • atomium: molecular modeller and file parser, capable of reading from and writing to .pdb, .cif and .mmtf files (Python lib) (standalone)
  • Lemon: a framework for rapidly mining structural information from the Protein Data Bank (standalone)
  • pdbTools: command line python scripts to manipulate PDB file (standalone)
  • CGRtools: Python Library for Molecule, Reaction and Condensed Graph of Reaction Processing (standalone)
  • PyBioMed: A python package for generating various molecular representations for chemicals, proteins, DNAs and their interactions (standalone)
  • ChemmineR (descriptors, QSAR, etc) standalone
  • RStudio: (standalone)
  • Weka(standalone)
  • CDK (descriptors, QSAR, etc)(standalone)
  • RDKIT (descriptors, QSAR, etc)(standalone)
  • Biopython: freely available tools for biological computation written in Python like text mining in PubMed, sequences, manipulate PDB files, etc (standalone)
  • WebMD: patient forum for text mining and list of drugs, side effects, overdose, images… (online)
  • E-Dragon: (descriptors, QSAR, etc, standalone and online)
  • Python.org: Learning python and more (training)
  • scikit-learn: machine learning in Python (standalone)
  • GHOST: Adjusting the Decision Threshold to Handle Imbalanced Data in Machine Learning (standalone)
  • CIME: ChemInformatics Model Explorer: exploratory analysis of chemical model explanations (standalone)
  • PubChemPy: provides a way to interact with PubChem in Python (standalone)
  • Pycharm: IDE (Integrated Development Environment) for Python (standalone)
  • Reticulate: R interface to Python (standalone)
  • PaDEL: (descriptors, QSAR, etc, standalone and online)
  • ProtDCal :descriptors for sequences and protein 3D-structures (online)
  • Rapidminer: Data science - machine learning (standalone)
  • Orange: Data science - machine learning (standalone)
  • scikit-learn: Machine Learning in Python (standalone)
  • ChemMine: Chemical clustering and analysis, descriptors (online)
  • ChemBioServer: Chemical clustering, descriptors (online)
  • iFeature (a python package and web server for features extraction and selection from protein and peptide sequences) (online)
  • PubMedMineR: R package with text-mining algorithms to analyze PubMed abstracts (standalone)
  • Carrot2: Open Source Results Clustering Engine that can automatically organise search results into topics. Carrot2 can query PubMed and allows boolean searching. DataViz (online)
  • VOSViewer: tool for constructing and visualising bibliometric networks based on journals, researchers or individual publications. DataViz (standalone)
  • Voyant: web-based text analysis tool with a variety of functions. Search results from databases can be uploaded to the tool to show word frequency, words in phrases and word trending. DataViz (online)
  • Text analyser: Drag and drop full text articles and the tool will analyse the text and identify the key topics. DataViz (online)
  • PolySearch2: text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more (online)
  • BioReader: Text mining and classification on pubmed abstract (online)
  • PubReMiner: When you submit your query (which can be any query that can be processed by PubMed), PubReMiner will process the result of that query and display its results in frequency tables, which can be added/excluded from the query to optimize the results (online)
  • Medline Ranker: Text classification (online)
  • BioSeq-Analysis 2.0: analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches (online and standalone)
  • Mold2 (descriptors from a two-dimensional chemical structure) (standalone)
  • PyDPI: Freely Available Python Package for Chemoinformatics, Bioinformatics, and Chemogenomics Studies (descriptors proteins, ligands, computation of fingerprints...) (standalone)
  • NetGO 2.0: improving large-scale protein function prediction with massive network information (online)
  • Pergola-web: web server for the visualization and analysis of longitudinal behavioral data using repurposed genomics tools and standards (dataviz, online) (online)
  • ActLSmaps: Activity Landscape Plotter: A Web-Based Application for the Analysis of Structure–Activity Relationships (online)
  • Data Retrieval Knime: A new semi-automated workflow for chemical data retrieval and quality checking for modeling applications (knime) (standalone)
  • ResponseNet V3: revealing signaling and regulatory pathways connecting your proteins and genes across human tissues (online)
  • VOLPES: an interactive web-based tool for visualizing and comparing physicochemical properties of biological sequences, descriptors (online)
  • web-rMKL: a web server for dimensionality reduction and sample clustering of multi-view data based on unsupervised multiple kernel learning (online)
  • VOLPES: an interactive web-based tool for visualizing and comparing physicochemical properties of biological sequences, descriptors (online)
  • BEERE: server for biomedical entity expansion, ranking and explorations (online)
  • STITCH: Chemical-Protein Interaction Networks (drug-target interactions (DTI)) (online)
  • PubTator central: automated concept annotation for biomedical full text articles, text mining (online)
  • PathMe: merging and exploring mechanistic pathway knowledge. Allows users to comprehensively explore pathway crosstalk and compare areas of consensus and discrepancies (python, standalone and online)
  • 3D-e-Chem Nodes for KNIME: The nodes complement existing cheminformatics and bioinformatics nodes to enable the efficient exploitation of structural and pharmacological protein-ligand interaction data from proteome-wide databases (including kinases, GPCRs…) (standalone)
  • CD-HIT: clustering and comparing protein or nucleotide sequences (redundant sequences... for machine learning...) (online)
  • TeachOpenCADD KNIME workflows: teaching chemoinformatics with Knime, also available via Jupyter Notebooks, but RDKIT requires, good luck with the installation of RDKIT some some OS (standalone)
  • COVER: Conformational Oversampling as Data Augmentation for Molecules (standalone)
  • RAACBook: a web server of reduced amino acid alphabet for sequence-dependent inference by using Chou's five-step rule (online)
  • BioDataome: Download, preprocess, annotate and analyze omics data sets (online)
  • RESOLVED2: Prediction of Drug Approval After Phase I Clinical Trials in Oncology (online)
  • rstoolbox: a Python library for large-scale analysis of computational protein design data and structural bioinformatics (standalone)
  • PISCES: server for creating non-redundant lists of proteins. Generates PDB list by sequence identity and structural quality criteria (online)
  • FP2VEC: a new molecular featurizer for learning molecular properties (combination of FP2VEC and CNN model can achieve competitive results in many QSAR tasks, eg, Tox21, eSOL) (standalone)
  • MeTeOR: Literature mining and automated hypothesis-generation with MeTeOR. Discovery of disease- and drug-specific pathways through community structures of a literature network (online)
  • DynaVenn: web-based computation of the most significant overlap between ordered sets - Venn - Dataviz (online)
  • BCSExplorer: a customized biosynthetic chemical space explorer with multifunctional objective function analysis (online)
  • RADER: a RApid DEcoy Retriever to facilitate decoy based assessment of virtual screening (online)
  • Dash-Bio: A free, open-source Python library for bioinformatics and drug development applications (dataviz) (standalone) (standalone)
  • Dash-Bio: examples online, sequence analysis
  • Dash-Bio: examples of app (standalone)
  • UniprotR: Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProt knowledgebase) (standalone)
  • Tableone: An Open Source Python Package for Producing Summary Statistics for Research Papers (text mining, standalone)
  • Trial2rev: Combining Machine Learning and Crowd-Sourcing to Create a Shared Space for Updating Systematic Reviews (text mining, online)
  • Dask: Scalable analytics in Python (to deal with large datasets not possible to handle with Pandas) (standalone)
  • MUBD-DecoyMaker 2.0: A Python GUI application to generate maximal unbiased benchmarking data sets for virtual drug screening (Windows, standalone)
  • Topoly: Python package to analyze topology of polymers (Python, standalone)
  • Hypopt: Parallelized grid search hyper-parameter optimization using a validation set (defaults to cross validation when no external validation set is available) (machine learning) (Python standalone)
  • gcForest: Python implementation of deep forest method (standalone)
  • OpenChem: A Deep Learning Toolkit for Computational Chemistry and Drug Design (needs RDKIT) (standalone)
  • DeepCoy: Generating Property-Matched Decoy Molecules Using Deep Learning (sets decoys for benchmarking and training) (standalone)
  • tpot: A Python Automated Machine Learning tool that optimizes machine learning pipelines using genetic programming (online)
  • Shapash: Python library which aims to make machine learning interpretable and understandable by everyone (standalone)
  • DECIMER-Segmentation: Automated extraction of chemical structure depictions from scientific literature (online)
  • MolFinder: an evolutionary algorithm for the global optimization of molecular properties and the extensive exploration of chemical space using SMILES (standalone)
  • KnowTox: pipeline and case study for confident prediction of potential toxic effects of compounds in early phases of development (standalone)
  • Worldometers-Coronavirus: Meta-MUMS COVID-19 web server, an online daily monitoring server for comparative and cumulative epidemiological analysis (online)
  • DescribePROT: Database of amino acid-level protein structure and function predictions, protein descriptors (online)
  • PySmash: Automatic substructure derivation and screening (toxicophore derivation, privileged motif detection (standalone)
  • Bionoi: Generate Voronoi representations of ligand-binding sites in proteins for machine learning applications (standalone)
  • Flame: an open source framework for model development, hosting, and usage in production environments (standalone)
  • BioReader: a text mining tool for performing classification of biomedical literature (Text mining, abstract) (online)
  • pssRNAit: Designing Effective and Specific Plant siRNAs with Genome-Wide Off-Target Assessment (online)
  • RANDOM.ORG: Introduction to Randomness and Random Numbers (online)
  • IMMAN: (Information theory- based CheMoMetrics ANalysis): user-friendly graphical interface for the computation of a collection of information- theoretic functions adapted for rank-based unsupervised and supervised feature selection tasks (standalone)
  • RAACBook: a web server of reduced amino acid alphabet for sequence-dependent inference by using Chou's five-step rule (molecular descriptors) (online)
  • SmilesPE: SMILES Pair Encoding: A Data-Driven Substructure Tokenization Algorithm for Deep Learning (standalone)
  • IDSM ChemWebRDF: SPARQLing small-molecule datasets. Resource Description Framework (RDF), together with well-defined ontologies, significantly increases data interoperability and usability. The SPARQL query language was introduced to retrieve requested RDF data and to explore links between them (standalone)
  • ChemDataExtractor: Automatically extract chemical information from scientific documents (standalone)
  • Practical Cheminformatics: blog to discuss chemoinformatics and medchem with some tutorials (online)
  • XGNNBOOST: XGBOOST is an algorithm combining GNN and XGBOOST, which can introduce the machine learning algorithm XGBOOST under the existing GNN network architecture to improve the algorithm capability (standalone)
  • LitSuggest: a web-based system for literature recommendation and curation using machine learning (text mining) (online)
  • OdoriFy: A conglomerate of Artificial Intelligence-driven prediction engines for olfactory decoding (online)
  • PaperScraper: facilitates scraping publication metadata from PubMed or from preprint servers such as arXiv, medRxiv, bioRxiv or chemRiv (text mining) (python standalone)
  • Mybinder.org: Turn a Git repo into a collection of interactive notebooks. With Binder, open those notebooks in an executable environment, make the code immediately reproducible by anyone, anywhere (code and data sharing) (online)
  • CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations (standalone and online)
  • Target2DeNovoDrug: molecule candidates for a target (standalone)
  • Assay Central: A New Approach to Compiling Big Data and Preparing Machine Learning Models (online)
  • Netwulf: Simple and interactive network visualization in Python (standalone)
  • FLAML: A fast and lightweight AutoML library (standalone)
  • GenUI: framework provides both API and GUI for molecular generators, QSAR modelling and chemical space visualization (standalone)
  • EXTRACT: Named entity recognition (text mining) (standalone)
  • DISEASES: Information extraction (cooccurrence-based information extraction) (text mining) (standalone)
  • ARROWSMITH: Knowledge discovery (eg, Two-Node Literature Search on articles present in MEDLINE, term B can provide a plausible connection between A and C; possible to apply semantic filters) (text mining) (standalone)
  • Europe PMC: Text mining (online)
  • DeepMol: a python-based machine and deep learning framework for drug discovery (standalone)
  • PadelPy: A Python wrapper for PaDEL-Descriptor software (standalone)
  • DMAKit: A user-friendly web platform for bringing state-of-the-art data analysis techniques to non-specific users (online) (standalone GitHub)
  • PyG: a library built upon PyTorch to easily write and train Graph Neural Networks for a wide range of applications related to structured data (standalone)
  • DGL-LifeSci: An Open-Source Toolkit for Deep Learning on Graphs in Life Science (standalone)
  • ssbio: a Python framework for structural systems biology (standalone)
  • Spiralize: an R package for visualizing data on spirals (standalone)
  • Biobox: a toolbox for biomolecular modelling (standalone)
  • Unipept Visualizations: an interactive visualization library for biological data (standalone)
  • AMPL: A Data-Driven Modeling Pipeline for Drug Discovery (ATOM Modeling PipeLine) (standalone)
  • MolVS: Molecule Validation and Standardization (standalone)
  • sdfconf: python package aimed to be used as a manipulation and analysis tool when working with .sdf files. High emphasis is on files with multiple conformations of molecules (standalone)
  • COKE: COVID-19 Knowledge Extractor: A Curated Repository of Drug−Target Associations Extracted from the CORD-19 Corpus ofScientific Publications on COVID-19 (online)
  • COKE: COVID-19 Knowledge Extractor: A Curated Repository of Drug−Target Associations Extracted from the CORD-19 Corpus ofScientific Publications on COVID-19 (standalone)
  • LEADD: Lamarckian evolutionary algorithm for de novo drug design (standalone)
  • GuacaMol: open source Python package for benchmarking of models for de novo molecular design (standalone)
  • DUD-E: an enhanced and rebuilt version of DUD, a directory of useful decoys. DUD-E is designed to help benchmark molecular docking programs by providing challenging decoys (dataset)
  • Enrichment-Plot: script to generate enrichment plot after virtual screening (standalone)
  • Molecule Generator: A fragment-based molecular generation method (standalone)
  • FRAGMENTISE: cross-platform tool to create and analyze comprehensive small-molecule fragment databases (standalone)
  • FRAGMENTISE: user guide (standalone)
  • MGCVAE: Multi-Objective Inverse Design via Molecular Graph Conditional Variational Autoencoder (standalone)
  • MolGPT: Molecular Generation using a Transformer-Decoder Model (standalone)
  • Chemspace Atlas: Multiscale Chemography of Ultralarge Libraries for Drug Discovery (online)
  • active-learning-drug-discovery: virtual screening (standalone)
  • FEPS: Feature Extraction from Protein Sequence (online)
  • FEPS_CFS: FEPS Complete Feature Set (FEPS_CFS) is a wrapper for the feature extraction tool (standalone)
  • DarkChem: employs a variational autoencoder (VAE) to learn a continuous numerical, or latent, representation of molecular structure, to simultaneously characterize and expand reference libraries (standalone)
  • GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics (standalone)
  • EvoMol: a flexible and interpretable evolutionary algorithm for unbiased de novo molecular generation (standalone)
  • CDDD: Continuous and Data-Driven Descriptors (standalone)
  • MSO: Molecular Swarm Optimization (standalone)
  • Streamlit: Build an app in a few lines of code (online)
  • Hiplot: a comprehensive and easy-to-use web service for boosting publication-ready biomedical data visualization (online)
  • CPRiL: Compound-Protein Relationships in Literature (text mining) (online)
  • MACAW: an accessible tool for molecular embedding and inverse molecular design (generative chemistry) (standalone)
  • MoLeR: a generative model of molecular graphs which supports scaffold-constrained generation (generative chemistry) (standalone)
  • NP_Fingerprints: Effectiveness of molecular fingerprints for exploring the chemical space of natural products (standalone)
  • Generative chemistry: conditional reduction of the loss value versus reinforcement learning for biassing a de-novo drug design generator (standalone)
  • PDBsum1: a standalone program for generating PDBsum analyses (standalone)
  • Pfeature: tools for computing protein and peptide features (online)
  • Pfeature: tools for computing protein and peptide features (standalone)
  • Pfeature: tools for computing protein and peptide features (standalone python Lib)
  • Pfeature: tools for computing protein and peptide features (standalone github)
  • rdkit-scripts: rdkit scripts making life easier (standalone)
  • GAN-Drug-Generator: Generative Adversarial Network for generation and optimization in targeted drug design (standalone)
  • BagPype: A Python package for the construction of atomistic, energy-weighted graphs from biomolecular structures (search for allosteric sites) (standalone)
  • ProteinLens: energy-weighted graph representation of a biomolecular structure and explores the long-range communication or connectivity between any specific sites in the system (identify potential allosteric sites, explore allosteric pathways, uses BagPype) (online)
  • Chemical Space dataviz: Visualizing chemical space networks with RDKit and NetworkX (standalone)
  • ProFeatX: A parallelized protein feature extraction suite for machine learning (PROtein FEATure eXtractor) (online)
  • ProFeatX: A parallelized protein feature extraction suite for machine learning (PROtein FEATure eXtractor) (standalone)
  • RAMAplot: python tool for Ramachandran plot (standalone)
  • MolScribe: Robust Molecular Structure Recognition with Image-to-Graph Generation (standalone)
  • iFeatureOmega: platform for the feature engineering, visualization and analysis of features from molecular sequence, structural and ligand data sets (standalone)
  • iFeatureOmega: platform for the feature engineering, visualization and analysis of features from molecular sequence, structural and ligand data sets (online)
  • Breeze: a web application for drug screening data analysis (online)
  • TeachOpenCADD: open courses - training in CADD by Prof. Volkamer et al. (standalone)
  • AI4Chemistry: open courses - training in ML and AI (standalone)
  • Practical Deep Learning: open courses - training in ML and AI (standalone)
  • Machine Learning: Backpropagation (standalone)
  • Machine Learning: Deep learning for molecules (standalone)
  • Computer methods: training, python, molecular modeling (standalone)
  • Practical Chemoinformatics: tutorials in chemoinformatics (standalone)
  • ML: machine learning (standalone)
  • ARAX: a graph-based modular reasoning tool for translational biomedicine (online)
  • Biotite: Swiss army knife for bioinformatics (Python) (sequence, logo, UniProt and much much more)(standalone)
  • NN-SVG: drawing NN architectures and exporting SVG images (online)
  • Pymsaviz: a MSA(Multiple Sequence Alignment) visualization python package for sequence analysis implemented based on matplotlib (standalone)
  • hydrodispred: Accurate Prediction of Disordered Regions in Proteins (Hydrophobicity) (online)
  • PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank (standalone)
  • PDB-BRE: A ligand-protein interaction binding residue extractor based on Protein Data Bank (standalone)
  • UMAP-compound-clustering: utilities (standalone)
  • IntraSOM: Python-based implementation of self-organizing maps (SOM) developed by the Integrated Technology for Rock and Fluid Analysis (InTRA) research center (standalone)
  • Scikit-mol: Scikit-Learn classes for molecular vectorization using RDKit (standalone)
  • gpt-repository-loader: Prepare files for GPTs (standalone)
  • LMstudio: Discover, download, and run local LLMs (LLMs, standalone)
  • Ollama: Get up and running with large language models, locally (LLMs, standalone)
  • crewAI: Cutting-edge framework for orchestrating role-playing, autonomous AI agents (LLMs, standalone)
  • DescriptaStorus: compute small molecule descriptors for machine learning (standalone)
  • Green Algorithms: Environmentally Sustainable Computational Research (online)
  • Merge-LLM: Merge Large Language Models (standalone)
  • AutoGluon: Automates machine learning tasks - Multimodal AutoML for Image, Text, Time Series, and Tabular Data (standalone)
  • Chemprop: a repository containing message passing neural networks for molecular property prediction (standalone)
  • smiles-encoder: One-hot encoding for simple molecular-input line-entry system (SMILES) strings (standalone)