Computer tools and databases

This page contains over 2500 links, mainly for macromolecules. URLs were cleaned and dead links removed in November 2025.

2D molecular visualization (chemicals, macromolecules, network)

• Cytoscape Web: bringing network biology to the browser (online)
• NetMedPy: A Python package for Large-Scale Network Medicine Screening (standalone)
• LeView: protein-ligand (standalone)
• ChemPixCH: Hand Drawn Hydrocarbon Recognition (image to smiles) (standalone)
• OpenChemIE: open source toolkit for extracting molecule or reaction data from figures or text (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)
• 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)
• 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)
• TMRPres2D: TransMembrane protein Re-Presentation in 2 Dimensions (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)
• 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 4.0: faster residue interaction networks with novel interaction types across over 35,000 different chemical structures (online, 2024).
• RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles (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)
• LigPlot+: view protein-ligand interactions in 2D (standalone)
• Cell Signaling: pathways, data visualization (online)

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

• ProSECFPs: A Novel Fingerprint-Based Protein Representation Method for Missense Mutation Pathogenicity Prediction (standalone, 2025).
• DeepProtein: Deep learning library and benchmark for protein sequence learning (AI tool)(standalone).
• DIRseq: a method for predicting drug-interacting residues of intrinsically disordered proteins from sequences (standalone, 2025).
• PaleAle 6.0: Prediction of Protein Relative Solvent Accessibility by Leveraging Pre-Trained Language Models (standalone, 2025).
• MMseqs2: Ultra fast and sensitive sequence search and clustering suite (standalone).
• 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)
• AIUPred: combining energy estimation with deep learning for the enhanced prediction of protein disorder (online).
• ALBATROSS: A deep-Learning Based Approach for predicTing pRoperties Of diSordered proteinS (online, 2024).
• metapredict: a deep-learning based consensus predictor of intrinsic disorder and predicted structure (online).
• pyMSA: Scoring Multiple Sequence Alignments with Python (standalone).
• sparrow: a tool for integrative analysis and prediction from protein sequence data (standalone).
• CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins (online).
• SLiMAn 2.0: Short Linear Motif Analysis (online, 2024).
• FuzPred: a web server for the sequence-based prediction of the context-dependent binding modes of proteins (online, 2024).
• DisoFLAG: accurate prediction of protein intrinsic disorder and its functions using graph-based interaction protein language model (online, 2024).
• COMER: protein analysis by homology (online)
• NetSurfP: accurate and fast prediction of protein structural features by protein language models and deep learning (online)
• DeepPredict: a state-of-the-art web server for protein secondary structure and relative solvent accessibility prediction (online, 2025)
• 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)
• 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)
• 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)
• Protein Residue Conservation Prediction: needs aligned sequence as input (Bioinformatics, 23(15):1875-82, 2007)
• ProtrWeb: Compute Protein Sequence-Derived Structural and Physicochemical Descriptors (input sequence) (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)
• 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)
• 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)
• 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)
• DeepIDP-2L: protein intrinsically disordered region prediction by combining convolutional attention network and hierarchical attention network (online)
• MoRFpred: Predicting Functions of Disordered Proteins (online)
• MAFFT (sequence alignment): online tool
• 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)
• 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)
• 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)
• 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)
• 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)
• PRALINE: multiple sequence alignment (online)
• Skylign: tool for creating logos representing both sequence alignments and profile hidden Markov models (generate logo) (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)
• 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

• UnityMol: a molecular visualization software built on the Unity3D game engine (standalone)
• FGNNSol: Protein Solubility Prediction Using Fused Graph Convolutional Networks and Improved Attention Networks with AlphaFold3-Derived Features (standalone 2026)
• PymolFold: PyMOL Plugin for API-Driven Structure Prediction and Quality Assessment (standalone 2025)
• IFPAggVis: Systematic analysis, aggregation and visualisation of interaction fingerprints for molecular dynamics simulation data (standalone)
• VTX: High performance molecular visualization software (Windows, Linux) (standalone 2025)
• 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)
• 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 2025: protein-ligand non covalent interactions and introducing protein–protein interactions to the protein–ligand interaction profiler (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)
• MOLEonline: provides a direct access to MOLE functionality and enables on-line and easy-to-use interactive channel analysis (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)
• 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)
• WebMolCS: server to visualize 3D Chemical Spaces (online and standalone)
• Web3DMol: view protein in 3D and sequences (online)
• 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.. Protein language models

• ProteinDJ: A high-performance and modular protein design pipeline (standalone 2026)
• DeepFold-PLM: Accelerating Protein Structure Prediction via Efficient Homology Search Using Protein Language Models (standalone, 2025).
• Prot2Chat: Protein LLM with Early-Fusion of Text, Sequence and Structure (e.g., Q&A about the possible function of a protein using a 3D structure and sequence as input) (standalone, 2025).
• Protenix: Protein structure prediction (related to AF3) (standalone, 2024).
• Protenix:: Protein structure prediction (related to AF3) (online, 2024).
• AlphaFold3: Accurate structure prediction of biomolecular interactions & protein structures (online, 2024).
• Assess: structure assessment web server for proteins, complexes and more (online, 2024).
• iQDeep: web server for protein scoring using multiscale deep learning models (evaluate quality of the 3D structure) (standalone)
• 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)
• Afpdb: efficient structure manipulation package for AI protein design (built on AlphaFold’s NumPy architecture, leverages RFDiffusion's contig syntax..addressing the limitations of existing tools like Biopython) (standalone, 2024).
• PDBFixer: application for fixing problems in PDB - Protein Data Bank files, missing residues, loop... (standalone)
• 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)
• 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)
• 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)
• 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)
• 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)
• 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)
• 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)
• Modelsearch : Search protein sequence in databases of 3D precomputed models (online)
• CABS-FOLD: de novo modeling, can also use alternative templates (consensus modeling) (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)
• 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)
• 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)
• HMMER: biosequence analysis using profile hidden Markov models (standalone)
• HMMER: (online)
• TCRmodel: high resolution modeling of T cell receptors from sequence (online)
• Mustguseal: Multiple Structure-Guided Sequence Alignment of Protein Families (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)
• 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)
• QUARK ab initio protein folding (online)
• (PS)2-v2: Protein Structure Prediction Server (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)
• HotSPOT Wizard: design mutations
• PDBeFold: 3D Structure Comparison (online)
• Dali: 3D Structure Comparison (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)
• VADAR (Validation of 3D structures) (online)
• ModFOLD9: 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)
• ProQ3 Validation of 3D structures (online)
• QMEAN Validation of 3D structures (standalone and 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

• Stack-OglyPred-PLM: Prediction of human O-linked glycosylation sites using stacked generalization and embeddings from pre-trained protein language model (standalone, 2024).
• 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)
• Glycosylator: a Python framework for the rapid modeling of glycans (standalone)
• 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)
• Glycomics@ExPASy: glycoinformatics (online)
• UniCarbKB: online information storage and search platform for glycomics, carbohydrates and glycobiology research (online)

Antibody modeling and related (eg., vaccine)

• GeoGAD: Geometry-Aware Antibody Design Framework for Complementarity-Determining Region Precision Engineering (standalone 2026)
• Origin-1: a generative AI platform for de novo antibody design against novel epitopes (standalone 2026)
• EvolveX: In silico design of stable single-domain antibodies with high affinity (standalone 2026)
• Ab-SELDON: Leveraging Diversity Data for an Efficient Automated Computational Pipeline for Antibody Design (standalone 2026)
• HeavyBuilder: Analysis of High-Throughput of Antibody Heavy Chain Repertoires in the Structural Space (standalone 2025)
• Boltzgen: universal binder design (standalone 2025)
• ODesign: A World Model for Biomolecular Interaction Design (design peptides, small molecules, proteins...) (standalone, 2025).
• DiscoTope-3.0: Improved B-cell epitope prediction using AlphaFold2 modeling and inverse folding latent representations (online).
• DeepAb: Antibody structure prediction using interpretable deep learning (standalone).
• EpitopeVec: linear epitope prediction using deep protein sequence embeddings (standalone).
• epitope3D: a machine learning method for conformational B-cell epitope prediction (online).
• SCALOP: Sequence-based antibody Canonical LOoP structure annotation (standalone).
• AbAgIntPre: CNN-based tool, predicts antibody-anti-gen interactions (online).
• ALLM-Ab: Active Learning-Driven Antibody Optimization Using Fine-tuned Protein Language Models (standalone 2025)
• ANABAG: Annotated Antibody–Antigen Data Set with Unique Features for Antibody Engineering Applications - Scripts (standalone, 2025).
• ANABAG: Annotated Antibody–Antigen Data Set with Unique Features for Antibody Engineering Applications - Data (standalone, 2025).
• MMCDP: Significantly enhancing human antibody affinity via deep learning and computational biology-guided single-point mutations (standalone, 2025).
• MMCDP (data): Significantly enhancing human antibody affinity via deep learning and computational biology-guided single-point mutations (standalone, 2025, DATA for MMCDP).
• MultiSAAl: Sequence-informed Antibody-Antigen Interactions Prediction using Multi-scale Deep Learning (online, 2025).
• ProtAttBA: Sequence-Only Prediction of Binding Affinity Changes (standalone, 2025).
• HAIRpred: Prediction of human antibody interacting residues in an antigen from its primary structure (online, 2025).
• hAb-Convergent: an antibody rearrangement analysis system for therapeutic antibody engineering based on convergent evolution (online). 2025.
• DeepNano: tool for predicting nanobody-antigen interactions (standalone).
• p-IgGen: A paired antibody generative language model (standalone, 2024).
• https://github.com/Exscientia/ABodyBuilder3: improved and scalable antibody structure predictions (standalone, 2024).
• VCAb: a web-tool for structure-guided exploration of antibodies (standalone).
• Exscientia-ab-characterisation: Computational design of developable therapeutic antibodies: efficient traversal of binder landscapes and rescue of escape mutations (standalone, 2024).
• ANARCI: Antibody Numbering and Antigen Receptor ClassIfication (standalone).
• HADDOCK3: Towards the accurate modelling of antibody-antigen complexes from sequence using machine learning and information-driven docking (standalone, 2024).
• ISPIPab: Computational Prediction of Multiple Antigen Epitopes (standalone, 2024).
• EpiScan: accurate high-throughput mapping of antibody-specific epitopes using sequence information (standalone)
• AntiBERTy: an antibody-specific transformer language model pre-trained on 558M natural antibody sequences (standalone)
• AbLang-2: Addressing the antibody germline bias and its effect on language models for improved antibody design (standalone)
• Locuaz: An in-silico platform for protein binders optimization (standalone, 2024).
• GEP: Geometric Epitope and Paratope Prediction (standalone, 2024)
• 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)
• 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)
• 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)
• BepiPred-3.0: Improved B-cell epitope prediction using protein language models (online)
• The Antibody Registry: Ten years of registering antibodies (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)
• 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)
• 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)
• MMDB: Biggest database of antibody, HLA and TCR crystallography structures (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)
• 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)
• 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)
• 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)
• SmrtMolAntibody: commercial tool
• TABS: Therapeutic Antibody Database (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)
• 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)
• 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)
• ModRefiner :algorithm for atomic-level, high-resolution protein structure refinement (online)
• GPCR-I-TASSER: computational method designed for 3D structure prediction of G protein-coupled receptors (online)
• pyGOMoDo: GPCRs modeling and docking with python (standalone)

Protein-protein docking and related

• EuDockScore: Euclidean graph neural networks for scoring protein-protein interfaces
• HADDOCK3: High Ambiguity Driven protein-protein DOCKing (full Python) (standalone, 2024).
• ModFOLDdock: quality assessment servers (online).
• Locuaz: An in-silico platform for protein binders optimization (standalone, 2024).
• 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)
• 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)
• 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
• 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)
• DOCKSCORE: rank docked poses (online)
• InterEvDock2: protein docking using evolutionary and biological information from homology models and multimeric inputs (online)
• webSDA: Simulation of Diffusional Assosiation (SDA) (online)
• FRODOCK: Fast Rotational DOCKing (online)
• ZDOCK: docking (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 2.4: High Ambiguity Driven protein-protein DOCKing (online requires login)
• Cluspro: protein docking (online)
• ClusPro-DC: discrimination between Xray and biological dimers (online requires login)
• 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

• DeepOrienter: Deep orienter of protein-protein interaction networks (standalone, 2024).
• 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).
• 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)
• 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)
• 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)
• 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)
• 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: protein-protein interaction prediction system (standalone)
• 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)
• 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
• 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

• MPBind: Multitask Protein Binding Site Prediction by Protein Language Models and Equivariant Graph Neural Networks (standalone 2025)
• FACE2FACE: Fast, Comprehensive, and User Customizable Macromolecule Interface Analysis (online, 2025).
• PPInterface dataset: contains about 815000 interface structures (online, 2024).
• PIE: Protein interaction explorer to navigate Protein-Protein interactions and ligand binding pockets (online, 2024).
• DeepUMQA3: a web server for accurate assessment of interface residue accuracy in protein complexes (online)
• PEPPI: protein-protein interaction predictions (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)
• PCPIP: Classification and prediction of protein-protein interaction interface using machine learning algorithm (online)
• 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)
• PCRPi: Integrates diverse metrics into a unique probabilistic measure (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)
• 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)
• 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)
• DIBS: a repository of disordered binding sites mediating interactions with ordered proteins - database (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
• 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)
• 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)
• iLoops: predict interactions (online
• SPRING: template-base algorithm for protein-protein complex structure prediction (online)

Protein-membrane (transient or not)

• TmDet 4.0: determining membrane orientation of transmembrane proteins from 3D structure (online), 2025.
• 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)
• 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)
• PPM server: calculates rotational and translational positions of transmembrane and peripheral proteins in membranes using their 3D structure (PDB coordinate file) as input (online)
• INSert membrANE (INSANE) - coarse grain Martini (standalone)
• (Pro)tein (B)ilayer (L)ipid (M)embrane (ProBLM)
• MemProtMD (Membrane-embedded structures), database of around 3500 intrinsic membrane protein structures (online)
• FATSLiM: to analyze MD simulations of membranes (standalone)
• OPM-DB (prepare protein-membrane systems) online
• Protter (interactive protein feature visualization, online)
• TOPCONS: Consensus prediction of membrane protein topology and signal peptides (online)
• DGpred: deltaG prediction for TM helix insertion (online)
• CELLmicrocosmos MembraneEditor: online and standalone

Molecular simulation - refinement - flexibility (mainly macromolecules)

• ProTDyn: a foundation Protein language model for Thermodynamics and Dynamics generation (standalone 2025)
• aSAM: Deep generative modeling of temperature-dependent structural ensembles of proteins - aSAM (atomistic structural autoencoder model - latent diffusion model) (standalone 2025)
• AlphaFlow: AlphaFold Meets Flow Matching for Generating Protein Ensembles (standalone)
• DynaMate: An Autonomous Agent for Protein-Ligand Molecular Dynamics Simulations (standalone 2025)
• ExEnDiff: An Experiment-guided Diffusion model for protein conformational Ensemble generation (standalone 2025)
• BioEmu: Biomolecular Emulator, a model that samples from the approximated equilibrium distribution of structures for a protein monomer, given its AA sequence (standalone)
• Deep-GIST: Deep Learning Models for Predicting the Distribution of Hydration Thermodynamics around Proteins (standalone 2026)
• fdGaMD: Fragment-dissolved Gaussian-accelerated-Molecular-Dynamics (standalone 2025)
• Gromacs MetaDump: a tool for extracting GROMACS simulation metadata (online, API and standalone 2025)
• MPBuild: Automated Membrane Protein System Construction Toolkit (standalone 2025)
• Clustering_Networks: Clustering and Analyzing Ensembles of Residue Interaction Networks from Molecular Dynamics Simulations (standalone, 2025).
• MDPath: Unraveling Allosteric Communication Paths of Drug Targets through Molecular Dynamics Simulations (standalone, 2025).
• PEGASUS: Prediction of MD-derived protein flexibility from sequence (standalone, 2025).
• PEGASUS: Prediction of MD-derived protein flexibility from sequence (online, 2025).
• EasyMD: Python package that simplifies molecular dynamics simulations (standalone, 2025).
• Memprot.GPCR-ModSim: Modelling and simulation of membrane proteins in a nutshell (standalone, 2024).
• Memprot.GPCR-ModSim: Modelling and simulation of membrane proteins in a nutshell (online, 2024).
• mdapy: Molecular Dynamics Analysis with Python (standalone).
• TrajMap.py: Trajectory maps: molecular dynamics visualization and analysis (standalone).
• MDiGest: A Python package for describing allostery from molecular dynamics simulations (standalone).
• CosolvKit: Python package for creating cosolvent system (standalone, 2024).
• ADOPT: Attention based DisOrder PredicTor (standalone, 2024).
• ConfDiff: Protein Conformation Generation via Force-Guided SE(3) Diffusion Models (standalone, 2024).
• WARIO: Weighted families of contact maps to characterize conformational ensembles of (highly-)flexible proteins (standalone, 2024).
• metadynminerpy: Analysis of metadynamics simulations by metadynminerpy (standalone, 2024).
• UFConf: Accurate Conformation Sampling via Protein Structural Diffusion (standalone, 2024).
• AllosES: Prediction of Protein Allosteric Sites with Transfer Entropy and Spatial Neighbor-Based Evolutionary Information Learned by an Ensemble Model (standalone, 2024).
• NRIMD: Analyzing Protein Allosteric Interactions Based on Molecular Dynamics Simulation (standalone, 2024).
• MolDy: Molecular dynamics simulation made easy (GROMACS) (standalone, 2024).
• EXCOGITO: to investigate the mapping problem in coarse-grained modelling of biomolecules (standalone, 2024).
• 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).
• 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 (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)
• 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)
• 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)
• 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 (many tools like WatFinder (water)) (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)
• 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 3.0 :fast simulations of flexibility of protein structures (online, 2025
• 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
• QwikMD MD with VMD and NAMD (standalone Mac, Linux, Windows, Supercomputers)
• WEBnm@ Web server and services for comparing protein flexibility
• FoldX (simulation, Alascan, mutation, peptides...loops)
• FoldX 5.0: Working with RNA, small molecules and a new graphical interface (standalone)
• 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
• Abalone: Molecular simulations with AMBER-ii force field, Molecular Dynamics folding
• 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)
• 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)
• 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: 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)
• LipidBuilder: The physicochemical properties of the different lipid species are essential for the structural and functional organization of the biological membrane and its interaction with integral and peripheral membrane proteins. online
• HTMD: a molecular-specific programmable environment to prepare, handle, simulate, visualize and analyze molecular systems (standalone)

Electrostatics of macromolecules - small molecules (...molecular surface properties)

• pyDelPhi: Accurate and Scalable Continuum Electrostatics for Large Biomolecular Systems (standalone, 2024).
• QupKake: Predict micro-pKa of organic molecules (standalone, 2024).
• pKa prediction: Accurate protein pKa prediction with physical organic chemistry guided 3D protein representation (online, 2024).
• 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)
• DispHScan: A Multi-Sequence Web Tool for Predicting Protein Disorder as a Function of pH (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)
• 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

• GlueFinder: A Data-Driven Framework for the Rational Discovery of Molecular Glues (standalone 2026)
• SwinSite: 3D Structure-Based Prediction of Protein−Ligand Binding Sites Using a Combined Vision Transformer and Convolution Model (standalone 2026)
• ErePOC: Deciphering DEL pocket patterns through contrastive learning. machine learning model to characterize and classify protein binding pockets to predict which proteins are suitable for DEL screening (standalone 2026)
• OPEF-MsL: Interpretable protein–small molecule binding site prediction via optimal PLM embedding fusion and multi-scale learning (standalone 2026)
• CDPKit: Binding Site Vectors Enable Mapping of Cytochrome P450 Functional Landscapes, python scripts gen_kuvek_bp_descr.py and cmp_kuvek_bp_descrs.py in the Chemical Data Processing Toolki (standalone 2026)
• DrugDomain 2.0: comprehensive database of protein domains-ligands/drugs interactions across the whole Protein Data Bank (standalone 2025)
• ALLSites: Accurate Identification of Protein Binding Sites for All Drug Modalities (standalone 2025)
• HOTPocket: The Human Omnibus of Targetable Pockets (standalone 2025)
• SiteMatcher: A Web Server for Structure-Based Drug Design Using Protein–Ligand Interaction Patterns (online, 2025)
• fdMD: An efficient method to locate binding sites: Fragment Dissolved Molecular Dynamics (standalone 2025)
• RAPID-Net: Accurate Pocket Identification for Binding-Site-Agnostic Docking (standalone 2025)
• HOTPocket: The human omnibus of targetable pockets (standalone 2025).
• CryptoBench: cryptic protein–ligand binding sites dataset and benchmark (standalone 2025).
• SLiPP: A Machine Learning Model for the Proteome-Wide Prediction of Lipid-Interacting Proteins (standalone 2025).
• Allofusion: Allosteric Site Prediction Based on Language Models and Multi-Feature Fusion (standalone 2025).
• NanoShaperWeb: Molecular Surface and Pocket Detection Made Visual (numerous computations on pockets) (online).
• PLINDER: The protein-ligand interactions dataset and evaluation resource (standalone).
• Epocs: Mapping the space of protein binding sites with sequence-based protein language models (standalone).
• LIGYSIS-web: a resource for the analysis of protein-ligand binding sites (also in Github) (online).
• Deepallo: A Deep Learning Framework for Allosteric Site Prediction (standalone).
• VirtuousPocketome: Tool for Virtual Screening of Protein Structures to Identify Similar Binding Sites (standalone).
• PLINDER: the protein–ligand interactions dataset and evaluation resource (standalone, 2024).
• LBS-comparison: Comparative analysis of methods for the prediction of protein-ligand binding sites (curated reference dataset, LIGYSIS) (standalone, 2024).
• CLAPE-SMB: Protein-small molecule binding site prediction based on a pre-trained protein language model (standalone).
• E-FTMap: Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites (online, 2024).
• MEF-AlloSite: accurate and robust Multimodel Ensemble Feature selection Allosteric Site identification (standalone, 2024).
• PASSer2.0: accurate prediction of protein allosteric sites through automated machine learning (online).
• Large-Scale-Pocket-Tunnel-Annotation: Large-scale Annotation of Biochemically Relevant Pockets and Tunnels in Cognate Enzyme-Ligand Complexes (standalone, 2024).
• PocketVec: Comprehensive detection and characterization of human druggable pockets through binding site descriptors (standalone, 2024).
• ProSPECCTs: a collection of 10 datasets composed of protein-ligand binding site pairs classified as similar or dissimilar (dataset, 2024).
• PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins (standalone, 2024).
• Pocket_Detection: Protein ligand binding site prediction using graph transformer neural network (standalone, 2024).
• LVPocket: integrated 3D global-local information to protein binding pockets prediction with transfer learning of protein structure classification (standalone, 2024).
• PPI-ligands-pockets-dataset: A comprehensive dataset of protein-protein interactions and ligand binding pockets for advancing drug discovery (data, 2024).
• 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)
• 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)
• 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)
• 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)
• 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)
• 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)
• 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)
• Cysteine binder collection: Cysteine Focused Covalent Inhibitor Library (dataset, commercial)
• CovPDB: a high-resolution coverage of the covalent protein–ligand interactome (online database)
• 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)
• 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)
• 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)
• 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 2.0: analysis of tunnels and ligand transport in dynamic ensembles of proteins (online). 2025
• PrankWeb 4: a modular web server for protein–ligand binding site prediction and downstream analysis (online). 2025
• 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
• 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))
• AlloFinder :a strategy for allosteric modulator discovery and allosterome analyses (not for pocket but ligand) (online)
• Cryptoscout Predict cryptic sites and druggable cavities on a protein structure using mixed-solvent molecular dynamics simulations in presence of benzene (online)
• 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)
• 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)
• COACH: meta-method (COFACTOR, FINDSITE and ConCavity...) (online)
• TRAPP : a tool for analysis of transient binding pockets in proteins (online)
• AlloSite: allosteric site (online)
• ConCavity: prediction from protein sequence and structure (geometry-based) (online)
• SplitPocket: geometry-based (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)
• 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)
• 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)
• 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)
• COFACTOR: pocket comparison online
• Evolutionary Trace Annotation: (ETA) pocket comparison online
• fPOP: pocket comparison online
• Imaaagine: pocket comparison online)
• PDBSITE: PDBsitescan (pocket comparison online)
• pevoSOAR: (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)
• VLDPws (analyze surface & solvate - water) (online)
• PROPORES (Novel toolkit for identifying pockets, cavities and channels of protein structures) (standalone)
• EPOS_BP BALLPass (standalone)
• PatchSearch (compare pockets) (standalone)
• WaterDock-2.0 (PyMol) (standalone)
• WaterDock-2.0 (standalone)
• 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)
• 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)

Biostructural pathology - Structural analysis - Mutations

Variation - mutation databases

• COSMIC, COSMIC-3D...: Catalogue Of Somatic Mutations In Cancer
• 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)
• 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)
• 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)
• 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)
• AlloMAPS: allosteric mutation analysis and polymorphism of signaling database (online)
• HPA human protein atlas - cancer and pathology…
• Mouse Phenome Database : an integrative database and analysis suite for curated empirical phenotype data from laboratory mice
• mutation3D functional prediction and visualization for aa substitutions on protein models and structures
• dbGaP: The database of Genotypes and Phenotypes (dbGaP)
• dbNSFP
• ClinVar aggregates information about genomic variation and its relationship to human health (database online)
• Database of Genomic Structural variation
• European Variation Archive (EVA) Public variation
• 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

• Varity: Improved pathogenicity prediction for rare human missense variants (standalone 2021)
• PATHOS: Predicting Variant Pathogenicity by Combining Protein Language Models and Biological Features (online, 2026)
• ProSST: Protein Language Modeling (LLM - PLM) with Quantized Structure and Disentangled Attention (not specifically for mutation but can help gaining insights) (standalone)
• RSALOR: Residue conservation and solvent accessibility are (almost) all you need for predicting mutational effects in proteins (standalone)
• 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)
• EVE: Disease variant prediction with deep generative models of evolutionary data (online, 2021)
• DDAffinity: predicting the changes in binding affinity of multiple point mutations using protein 3D structure (standalone 2025).
• FIBOS: R and Python packages for analyzing protein packing and structure (standalone 2025).
• StructMAn 2.0 Web: a web server for structural annotation of protein sequences and mutations (online). 2025.
• DDGemb: predicting protein stability change upon single- and multi-point variations with embeddings and deep learning (online).
• VespaG: Expert-guided protein Language Models enable accurate and blazingly fast fitness prediction (mutation) (standalone, 2024).
• ProMEP: Zero-shot prediction of mutation effects on protein function with multimodal deep representation learning (standalone, 2024).
• ADOPT: intrinsic protein disorder prediction through deep bidirectional transformers (standalone, 2023).
• ADOPT: intrinsic protein disorder prediction through deep bidirectional transformers (online, 2023).
• DisPredict3.0: Prediction of intrinsically disordered regions/proteins using protein language model (online, 2024).
• ESM-Scan: Predict the impact of every possible mutation in any protein using Evolutionary Scale Modeling (saturation mutagenesis, no 3D) (standalone).
• THPLM: a sequence-based deep learning framework for protein stability changes prediction upon point variations using pretrained protein language model (standalone, 2023).
• MMPatho: Interpretable Model with Multilevel Consensus and Evolutionary Information for Missense Mutation Pathogenic Prediction and Annotation(standalone).
• VariPred: Enhancing missense variant pathogenicity prediction with protein language models using VariPred (standalone, 2024).
• SIGMA: leverages protein structural information to predict the pathogenicity of missense variants (standalone).
• Protein_Pretrain: Multimodal pretraining for unsupervised protein representation learning (standalone).
• BenchStab: a tool for automated querying of web-based stability predictors (standalone, 2024).
• AggreProt: Predicting and engineering aggregation prone regions in proteins (online, 2024).
• CORDAX: Platform for the prediction and 3D visualization of aggregation motifs in protein sequences (online, 2024).
• PredictOnco: A computational workflow for analysis of missense mutations in precision oncology (standalone, 2024).
• Locuaz: An in-silico platform for protein binders optimization (standalone, 2024).
• PLM4Muts: enhancing predictions of protein stability changes induced by single mutations using MSA-based Language Models (standalone, 2024).
• AggreProt: server for predicting and engineering aggregation prone regions in proteins (online, 2024).
• DDMut-PPI: predicting effects of mutations on protein-protein interactions using graph-based deep learning (online).
• ProtVar: mapping and contextualizing human missense variation (online, 2024).
• 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)
• 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)
• 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)
• 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)
• PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences (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)
• 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)
• 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)
• 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)
• 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)
• 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)
• Modict: Convert your favorite protein modeling program into a mutation predictor, uses rmsd and others (standalone)
• 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)
• 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)
• 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)
• mutfunc: Precomputed mechanistic consequences of mutations (online)
• MILAMP: Multiple Instance Prediction of Amyloid 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)
• 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
• TKSA-MC: A Web Server for rational mutation through the optimization of protein charge interactions (Tanford-Kirkwood Surface Accessibility model) (standalone on GitHub)
• 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)
• SNPnexus :assessing the functional relevance of genetic variation to facilitate the promise of precision medicine
• DynaMut :predicting the impact of mutations on protein conformation, flexibility and stability
• 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
• 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)
• 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)
• INPS-3D: protein stability (online)
• MOKCa: mutation hotspots in protein domains (cancer) (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)
• 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)
• 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)
• 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-seq: An online application for calculating folding free energy changes in proteins caused by missense mutations (online)
• DUET: stability change by combining two approaches
• I-Mutant2.0: Sequence and structure based (stability change)
• MuPro: Sequence and structure based (stability change)
• NeEMO: Residue interaction networks (stability change)
• PoPMuSiC: Structure based (stability change)
• FATHMM: mutation Sequence based
• Meta-SNP: Consensus classifier
• MutPred2: Sequence and structure-based
• PANTHER-PSEP: Sequence based
• Parepro: Sequence-based
• SIFT: Sequence-based
• SNPs&GO: Sequence and structure based
• VAPOR: Variant Analysis Consensus classifier
• PredictSNP2 (consensus)
• Cancer3D
• Plot protein: visualization of mutations
• ESBRI: salt bridges, electrostatics
• PROVEAN: Sequence and structure based
• PsychoProt: Physical CHemistry Of Protein variability
• Pharos: druggable genome - TCRD - (target central resource database))
• BindProf : deltadeltaG on PPI interface, needs a list of residue
• 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: contains human single nucleotide variations...
• mutLBSgeneDB: mutated binding pockets
• INPS-MD: predict stability
• 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)
• 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
• GenProBiS (mapping variants to protein binding sites)
• mCSM-DNA: aa changes on protein-nucleic acids
• SIFTS: integrate 3D structure, function, taxonomy & sequence, PDB-UniProt mapping)
• MAESTRO (multi agent stability prediction upon point mutations)
• mCSM: effect of mutations on stability, PPI, protein-DNA)
• 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

Peptide design, tox prediction

• PTP-SMGCA: Dual-Modal Fusion Based on Peptide Sequence and Molecular Graph with Bidirectional Cross-Attention for Precise Peptide Toxicity Prediction (standalone 2026)
• PepENS: An ensemble-based model comprising deep learning for predicting peptide-binding residues in proteins (standalone 2025)
• PepFoundry: A Pipeline for Building Machine-Learning Ready Representations of Nonstandard Peptides Containing Cycles, Non-natural Residues, Polymer Units, and More (standalone 2026)
• pepADMET: A Novel Computational Platform For Systematic ADMET Evaluation of Peptides (online 2026)
• PepGraphormer: an ESM-GAT hybrid deep learning framework for antimicrobial peptide prediction (standalone 2026)
• Peptide2Mol: A Diffusion Model for Generating Small Molecules as Peptide Mimics for Targeted Protein Binding (standalone 2025)
• PeptideGeneralizationBenchmarks: How to generalize machine learning models to both canonical and non-canonical peptides (standalone 2025)
• Boltzgen: universal binder design (standalone 2025)
• PepMSND: Integrating multi-level feature engineering and comprehensive databases to enhance in vitro/in vivo peptide blood stability prediction (standalone, 2025)
• PICKAPEP: An Application for Parameter Calculation and Visualization of Peptides (Windows, mac) (standalone)
• PepFuNN: Novo Nordisk Open-Source Toolkit to Enable Peptide in Silico Analysis (standalone)
• PandoraGAN: Generating antiviral peptides using Generative Adversarial Network (standalone)
• PepINVENT: Generative Peptide Design Beyond Natural Amino Acids (standalone)
• PepMNet: a hybrid deep learning model for predicting peptide properties using hierarchical graph representations (standalone 2024)
• PDGA: Peptide Design Genetic Algorithm is a modular genetic algorithm framework designed to generate peptide sequences with desired building blocks and properties (standalone)
• Peptide-GPT: Generative Design of Peptides using Generative Pre-trained Transformers and Bio-informatic Supervision (standalone)
• HELM-GPT: de novo macrocyclic peptide design using generative pre-trained transformer (standalone 2024)
• Datagrok: Peptides package provides tools for analyzing peptide structure-activity relationship (SAR) (commercial) (standalone 2024)
• ToxMSRC: Innovative peptide toxicity prediction model based on multi-scale convolutional neural network and residual connection (standalone, 2025)
• BenchmarkCycPeptMP: Systematic benchmarking of 13 AI methods for predicting cyclic peptide membrane permeability (standalone, 2025)
• GPepT: A Foundation Language Model for Peptidomimetics Incorporating Noncanonical Amino Acids (standalone, 2025)
• PepGenWL: A Unified Peptide Generative Framework via a Weakly Order-Dependent Autoregressive Language Model and Lifelong Learning (standalone, 2025).
• StackPIP: An Effective Computational Framework for Accurate and Balanced Identification of Proinflammatory Peptides (online, 2025).
• Ntxpred2: A large language model for predicting neurotoxic peptides and neurotoxins (standalone, 2025).
• Ntxpred2: A large language model for predicting neurotoxic peptides and neurotoxins (online, 2025).
• ToxiPep: Peptide toxicity prediction via fusion of context-aware representation and atomic-level graph (online).
• PeptideCLM: Peptide-Aware Chemical Language Model Successfully Predicts Membrane Diffusion of Cyclic Peptides (standalone).
• TPepPro: a deep learning model for predicting peptide-protein interactions (standalone, 2024).
• UniBioPAN: Classification Architecture for Bioactive Peptides Inspired by Video Action Recognition (standalone, 2024).
• UniBioPAN: Classification Architecture for Bioactive Peptides Inspired by Video Action Recognition (online, 2024).
• MD-LAIs: Computing Whole-Sequence and Amino Acid-Level “Embeddings” for Peptides and Proteins (standalone, 2024).
• StaPep: Toolkit for Structure Prediction, Feature Extraction, and Rational Design of Hydrocarbon-Stapled Peptides (standalone).
• DeepB3P: A Transformer-Based Model for Identifying and Generating Blood-Brain Barrier Penetrating Peptides by Using Feedback GAN (standalone).
• PepMLM: Target Sequence-Conditioned Generation of Peptide Binders via Masked Language Modeling (standalone).
• PepGLAD: Full-Atom Peptide Design with Geometric Latent Diffusion (standalone).
• PepPrCLIP: A new model for de novo design of peptide binders using deep learning and contrastive language modeling (standalone).
• IdpSAM: Transferable deep generative modeling of intrinsically disordered protein conformations (latent diffusion model for peptide conformation generation) (standalone).
• PepCNN: deep learning tool for predicting peptide binding residues in proteins using sequence, structural, and language model features (standalone, 2024).
• PeptideBERT: A Language Model Based on Transformers for Peptide Property Prediction (standalone, 2023).
• APD3 Antimicrobial Peptide Database: Databases and tools to analyze peptides (stability, enzyme cleavage sites...) (online).
• AMPDeep: hemolytic activity prediction of antimicrobial peptides using transfer learning (standalone, 2022).
• DeepB3P3: A prediction model for blood-brain barrier penetrating peptides based on masked peptide transformers with dynamic routing (standalone).
• CICERON: Classification of bIoaCtive pEptides fRom micrObial fermeNtation (standalone).
• DeepAIP: Deep Learning for Anti-inflammatory Peptide Prediction Using Pre-trained Protein Language Model Features Based on Contextual Self-Attention Network (standalone, 2024).
• PreAIP: Computational Prediction of Anti-inflammatory Peptides by Integrating Multiple Complementary Features (online)
• BertAIP: A BERT-based approach for identifying anti-inflammatory peptides using sequence information (standalone, 2024).
• PyAMPA: a high-throughput prediction and optimization tool for antimicrobial peptides (standalone).
• NeuroPP: A Tool for the Prediction of Neuropeptide Precursors Based on Optimal Sequence Composition (online).
• ToxTeller: Predicting Peptide Toxicity Using Four Different Machine Learning Approaches (standalone, 2024).
• PepNet: deep learning framework for predicting peptides with antimicrobial or anti-inflammatory activities by using a pretrained protein language model (standalone, 2024).
• LSTM_peptides: Recurrent Neural Network Model for Constructive Peptide Design (standalone).
• peptidy: python library to vectorize peptide sequences (and proteins) for machine learning, generate new peptides via LSTM (standalone).
• DeepPep: Deep-learning based bioactive therapeutic peptides generation (standalone).
• AutoPeptideML: AutoML system for building trustworthy peptide bioactivity predictors (standalone, 2024).
• HYDRA: A Hybrid Diffusion Model for Stable, Affinity-Driven, Receptor-Aware Peptide Generation (standalone, 2024).
• PGAT-ABPp: Harnessing Protein Language Models and Graph Attention Networks for Antibacterial Peptide Identification (standalone, 2024).
• ToxinPred 3.0: improved method for predicting the toxicity of peptides (standalone, 2024).
• ToxinPred 3.0: improved method for predicting the toxicity of peptides (online, 2024).
• HighFold: accurately predicting structures of cyclic peptides and complexes with head-to-tail and disulfide bridge constraints (standalone, 2024).
• Peptriever:a Bi-Encoder approach for large-scale protein-peptide binding search (sequence based protein-peptide binding search) (standalone, 2024).
• Peptriever:a Bi-Encoder approach for large-scale protein-peptide binding search (sequence based protein-peptide binding search) (online, 2024).
• 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)
• 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)
• 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)
• 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)
• 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)
• 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)
• Brainpeps: a resource of blood-brain barrier properties of peptides (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 (standalone) (dataset needed - ask the authors)
• 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)
• 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)
• 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)
• HLP: predicting half-life of peptides in intestine-like environment (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)
• COVID-19 Docking Server: An interactive server for docking small molecules, peptides and antibodies against potential targets of COVID-19 (online)
• 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)
• 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)
• 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)
• 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)
• 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)
• Pep-Fold peptide design 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)
• PEP-SiteFinder: A service to identify candidate protein-peptide interaction sites (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)
• GalaxyPepDock: Protein-peptide docking based on interaction similarity (online)
• BioPepDB repository of bioactive peptides (online)
• PhyreStorm (find related structure in the PDB) 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
• 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)
• 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)
• PEPlife (database of half life) online
• Rosetta: computational modeling and analysis of protein structures (online)
• 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)
• 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
• 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
• Protter (interactive protein feature visualization) online

Compound collections, medicinal drugs, pharmacology, protein databases

• Chembl_assay_annotation: Integrating artificial intelligence and manual curation to enhance bioassay annotations in ChEMBL (standalone 2026)
• NavDB: A Comprehensive Database for Voltage-Gated Sodium Channels Modulators and Targets (online 2026)
• ToxFCDB: Toxicity Database for Forever Chemicals (over 8,000 PFAS) (database online, 2026)
• dbAMP 3.0: updated resource of antimicrobial activity and structural annotation of peptides in the post-pandemic era (online, 2025) (running?)
• BFVD: a large repository of predicted viral protein structures (online, 2025)
• DRAMP 4.0: an open-access data repository dedicated to the clinical translation of antimicrobial peptides (online, 2025)
• DDInter 2.0: an enhanced drug interaction resource with expanded data coverage, new interaction types, and improved user interface (online, 2025)
• DrugMAP 2.0: molecular atlas and pharma-information of all drugs (online, 2025)
• ECBD: European chemical biology database (online, 2025)
• PDCdb: the biological activity and pharmaceutical information of peptide–drug conjugate (PDC) (online, 2025)
• MGTbind: a comprehensive database of molecular glue ternary interactome (online, 2025)
• Macrocycle-DB: a comprehensive database for macrocycle-based drug discovery (online, 2025)
• MolGlueDB: An online database of molecular glues (online, 2025).
• Veterinary-Drugs: Construction of the Veterinary DrugBank (online, 2025).
• TarKG: A Comprehensive Biomedical Knowledge Graph for Target Discovery (online, 2024).
• RepurposeDrugs: an interactive web-portal and predictive platform for repurposing mono- and combination therapies (standalone, 2024).
• DrugRepoBank: a comprehensive database and discovery platform for accelerating drug repositioning (online, 2024).
• BioLiP2: an updated structure database for biologically relevant ligand–protein interactions (online, 2024).
• SIU: A Million-Scale Structural Small Molecule-Protein Interaction Dataset for Unbiased Bioactivity Prediction (standalone, 2024).
• Pan-Canadian Chemical Library: Open Academic Chemistry to High-Throughput Virtual Screening (online, 2024).
• ChemoDOTS: a web server to design chemistry-driven focused libraries (Hit2lead) (online, 2024).
• 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)
• PROTAC-DB 3.0: an updated database of PROTACs with extended pharmacokinetic parameters (online, 2025)
• 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)
• CDEK: Clinical Drug Experience Knowledgebase (online)
• MolData: A Molecular Benchmark for Disease and Target Based Machine Learning (standalone)
• 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)
• COVIDium: a COVID-19 resource compendium (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)
• 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)
• 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)
• Brenda: The comprehensive enzyme information system (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)
• COVID-19 preVIEW: Semantic Search to Explore COVID-19 Research Preprints (text mining) (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)
• 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)
• 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)
• 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 2.0: a comprehensive database facilitating the discovery of covalent inhibitors (online, 2024)
• 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)
• NCATS COVID-19: high throughput screening data from the NCATS COVID-19 portal (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. More than 110 000 machine-readable pathways found in 10 model organisms. Small molecule hyperlinked to several public chemical databases such as HMDB or DrugBank and each protein or enzyme complex is hyperlinked to UniProt (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)
• 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)
• nAPOLI: a graph-based strategy to detect and visualize conserved protein-ligand interactions in large-scale (online)
• 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)
• 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)
• 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
• KinaMetrix: a web resource to investigate kinase conformations and inhibitor space (online)
• COD: Crystallography Open Database (online)
• NextProt: Exploring the universe of human proteins
• 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
• ApoCanD: Database of Human Apoptotic Proteins in the context of cancer
• 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)
• HIT 2.0: an enhanced platform for Herbal Ingredients' Targets (online)
• TCM Database@Taiwan: the world's largest traditional Chinese medicine database for drug screening in silico (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)
• SANCDB: a South African natural compound 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
• DiPPI: A curated dataset for drug-like molecules in protein-protein interfaces (data 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)
• 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)
• 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)
• 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)
• 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...)
• 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
• ECOdrug a database connecting drugs and conservation of their targets across species
• 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
• 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
• NPC Pharmaceutical Collection
• Molport: commercially-available compounds
• eMolecules: commercially-available compounds
• BioLiP: a semi-manually curated database for high-quality, biologically relevant ligand-protein binding interactions
• SWEETLEAD: An in silico database of approved drugs, regulated chemicals, and herbal isolates
• ProBis: pocket comparison online
• PDB: protein databank
• PDBe: protein databank europe
• PDBbind: comprehensive collection of the experimentally measured binding affinity data for all types of biomolecular complexes deposited in the Protein Data Bank (PDB)
• FDA Novel Drug Approvals (2021): a COVID-19 resource compendium (online)
• Binding DB: web-accessible database of measured binding affinities
• 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
• 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)
• PLINDER: the protein–ligand interactions dataset and evaluation resource (standalone, 2024).
• 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
• Cancer Cell Map Initiative (CCMI)
• DTome: Drug-Target Interactome
• LOINC (common language clinical and laboratory)
• Chemical Identifier Resolver (CIR)
• The Small Molecule Pathway Database (SMPDB)
• Fragment Database FDB-17 (10 million)
• TargetMine (tools for target prioritization)
• UniChem (cross-references between chemical structure identifiers from different databases)
• Drugs.com :data about drugs and clinical trials (check also drugs.com for drug-drug interactions, DDI), online
• DrugKiNET (kinase inhibitors)
• 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
  
  

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

• SciToolAgent: a knowledge-graph-driven scientific agent for multitool integration (standalone 2025)
• DrugPilot: LLM-based Parameterized Reasoning Agent for Drug Discovery (standalone 2024)
• dZiner: Rational Inverse Design of Materials with AI Agents (standalone 2024)
• CACTUS: Chemistry Agent Connecting Tool Usage to Science (standalone 2024)
• Prompt-to-Pill: Multi-Agent Drug Discovery and Clinical Simulation Pipeline (standalone 2026)
• CF-MF: Collision-free morgan fingerprints: a principled approach to enhance machine learning performance and interpretability in chemistry (standalone 2026)
• LigandExplorer: An Automated Tool for Ligand Extraction from PDB Structures (standalone 2026)
• MEHC-Curation: A Python Framework for High-Quality Molecular Dataset Curation (standalone 2026)
• RAKG: Document-level Retrieval Augmented Knowledge Graph Construction (standalone 2025)
• Selector: Python library for selecting diverse data subsets for machine-learning (standalone 2026)
• Multi-ViewSGT: Multi-Modal Fusion Frameworks of Subgraph-Optimized Graph Autoencoder for Molecular Property Prediction (standalone 2026)
• Smirk: Tokenization for Molecular Foundation Models - A Tokenizer for OpenSMILES (standalone, 2026)
• llm-text-to-knowledge-graph: Generation of Molecular Interaction Knowledge Graphs Using Large Language Models for Exploration in Cytoscape (standalone, 2026)
• libraryPDB: lightweight Python library for searching, downloading, parsing, cleaning and analyzing protein structures from the Protein Data Bank (standalone, 2025)
• ADvisor: An Open-Source Tool for Applicability Domain Definition and Optimization in Molecular Predictive Modeling (standalone, 2025)
• ChemDataExtractor 2.0: Automatically extract chemical information from scientific documents (standalone)
• 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)
• 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)
• 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)
• Wordclouds: Wordscloud (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)
• 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)
• 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)
• DENOPTIM: Software for Computational de Novo Design of Organic and Inorganic Molecules. Virtual compounds. Also utility to fragment small molecules (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)
• 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)
• 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)
• 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)
• PubMedMineR: R package with text-mining algorithms to analyze PubMed abstracts (standalone)
• 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)
• 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)
• BioSeq-Analysis 2.0: analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches (online and standalone)
• PyDPI: Freely Available Python Package for Chemoinformatics, Bioinformatics, and Chemogenomics Studies (descriptors proteins, ligands, computation of fingerprints...) (standalone)
• 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)
• VOLPES: an interactive web-based tool for visualizing and comparing physicochemical properties of biological sequences, descriptors (online)
• VOLPES: an interactive web-based tool for visualizing and comparing physicochemical properties of biological sequences, descriptors (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: A very widely used program for clustering and comparing protein or nucleotide sequences (eg for machine learning) (standalone)
• 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)
• 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)
• 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)
• 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)
• 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)
• RANDOM.ORG: Introduction to Randomness and Random Numbers (online)
• 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)
• 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)
• 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)
• 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)
• 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)
• 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 (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)
• 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)
• 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)
• 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)
• Breeze: a web application for drug screening data analysis (online)
• TeachOpenCADD: open courses - training in CADD by Prof. Volkamer et al. (standalone)
• RDKIT tuto: tuto for RDKIT (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)
• 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)
• 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)
• PETA: evaluating the impact of protein transfer learning with sub-word tokenization on downstream applications (standalone, 2024).
• CPIExtract: A software package to collect and harmonize small molecule and protein interactions (eg, from the PDB) (standalone, 2024).
• PANDA-3D: Protein function prediction based on AlphaFold models (online, 2024).
• PANDA-3D: Protein function prediction based on AlphaFold models (standalone, 2024).
• The-AI-Scientist: Towards Fully Automated Open-Ended Scientific Discovery (standalone, 2024).
• CURSOR: AI system to write code (commercial).
• Gotcha GPT: Ensuring the Integrity in Academic Writing (standalone, 2024).
• PaperQA2: language agents achieve superhuman synthesis of scientific knowledge (standalone, 2024).
• ProtChat: An AI Multi-Agent for Automated Protein Analysis Leveraging GPT-4 and Protein Multimodal Model (standalone).
• LLM-in-science: LLM in Biomed and chemistry (information, but not up to date now)
• OmniCLIC: a unified Omics Contrastive Learning framework for effective integration and classification of multi-omics data (standalone)

• bruno.villoutreix[at]gmail.com