Shortlist


If VLS3D is useful for your research (last update Nov. 17, 2019 and last URL cleaning, March 22, 2019)
Please cite: Villoutreix et al. Drug Discovery Today 2013, 18:1081-9

 

 

2D molecular visualization (chemicals & proteins)

  • LeView: protein-ligand (standalone)
  • CyTargetLinker: Extend biological networks (e.g., a disease network with Chembl or drugbank compounds) in Cytoscape (standalone)
  • PoseView: protein-ligand (online)
  • 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)
  • C-SPADE: web-application serves as an interactive and innovative visualization tool for drug screening data (online)
  • WebGraphviz: is Graphviz (Graphviz is open source graph visualization software) in the Browser (online)
  • PLEXVIEW: Make 2D diagrams of protein-ligand interactions (Hbonds, cation-pi) (online)
  • ezCADD: a Rapid 2D/3D Visualization Enabled Web Modeling Environment for Democratizing Computer-Aided Drug Design (small molecule docking, protein docking, 2D/3D interaction viz, de novo lead optimization, pocket search and polypharmacology) online
  • Chemicool: Periodic Table Key (online)
  • WebElements: Periodic Table Key (online)
  • ToxPi: ToxPi Graphical User Interface 2.0: Dynamic exploration, visualization, and sharing of integrated data models (standalone)
  • SmilesDrawer: parsing and drawing SMILES-encoded molecular structures using client-side JavaScript (standalone)
  • PathVisio: free open-source biological pathway analysis software that allows you to draw, edit and analyze biological pathways (standalone)
  • JME: JME Molecular Editor, draw and view chemicals (online)
  • PubChem Sketcher: A web-based tool for chemical sketching...(online)
  • Molinspiration: draw and view small molecules, predict 3D...(online)
  • Chemfig: draw molecules with easy syntax (standalone)
  • Chemtool: program for drawing chemical structures (standalone)
  • Molsketch: 2D molecular editing tool (standalone)
  • JChemPaint: chemical 2D structure editor (standalone)
  • SketchEl: interactive chemical molecule sketching tool (standalone)
  • BKchem: chemical drawing program (standalone)
  • DataWarrior: open-source data visualization and analysis program with embedded chemical intelligence (standalone)
  • NAViGaTOR: Network Analysis, Visualization, & Graphing TORonto (standalone)
  • Cytoscape: open source software platform for visualizing complex networks and integrating these with any type of attribute data (standalone)
  • Diversity Genie (analyze cmpds - collection diversity): powerful tool to analyze datasets of small organic molecules (standalone)
  • ChemAxon: software solutions and services for chemistry & 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)
  • cSeqLogo: Generation of consensus referenced two-sample Sequence Logos (online)
  • Topo2: transmembrane protein display (online)
  • TMRPres2D: TransMembrane protein Re-Presentation in 2 Dimensions (standalone)
  • Pro-origami: system for automatically generating protein structure cartoons in 2D (online)
  • CheS-Mapper: 3D-viewer for chemical datasets with small compounds (standalone)
  • FragVLib: Mining software for generating Fragment-based Virtual Library using pocket similarity search of ligand-receptor complexes (standalone)
  • ChemTreeMap : hierachical tree visualization of a molecule library (standalone)
  • Scaffold Hunter: software tool for the analysis of structure-related biochemical data (standalone)
  • RJSplot: Interactive Graphs with R (standalone)
  • OMNIDEPICT: 2D Chemical Depiction of Complex Molecules (SDG algorithm) (online)
  • ChemCom (compare compounds) (standalone)
  • MONGKIE: integrated network analysis and visualization platform for multi-omics data (standalone)
  • CellDesigner: a structured diagram editor for drawing gene-regulatory and biochemical networks (standalone)
  • RING (contact - residue interaction network) (online)
  • RINspector (a Cytoscape app for centrality analyses and DynaMine flexibility prediction with Chimera RINanalyser etc) (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 (online)
  • Protein Lounge: pathways (online)
  • Pathview Web: pathway visualization & data integration (online)
  • Minepath.org (interactive pathway analysis) (online)
  • LigPlot+ (view protein-ligand in 2D) (standalone)
  • Cell Signaling: pathways (online)

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

  • Multiple sequence alignment (MSA): alignment of three or more biological sequences (EMBL-EBI) (online)
  • Sourmash: Large-scale sequence comparisons (standalone)
  • Miew: 3D Molecular Viewer (standalone)
  • MAFFT-DASH: integrated protein sequence and structural alignment (online and standalone all OS)
  • GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters (online)
  • Phylogeny.fr: sequence searching, multiple sequence alignment, model selection, tree inference, tree drawing and a large panel of standard methods such as distance, parsimony, maximum likelihood and Bayesian (online)
  • PASTA 2.0: an improved server for protein aggregation prediction (online)
  • PSA: Pairwise (local) Sequence Alignment (EMBL-EBI) (online)
  • XSuLT: annotate an alignment with structural information in the form of formatting styles (online)
  • Prosat+: protein structure annotation (online)
  • MoRFpred: Predicting Functions of Disordered Proteins (online)
  • PTM-ssMP: Server for Predicting Different Types of Post-translational Modification Sites Using Novel Site-specific Modification Profile (online)
  • MAFFT (sequence alignment): (online)
  • iFeature: (a python package and web server for features extraction and selection from protein and peptide sequences) (online)
  • StructureMapper: a high-throughput algorithm for analyzing protein sequence locations in structural data (online)
  • BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra (online)
  • MPI Bioinformatics Toolkit: one-stop web service for protein bioinformatic analysis (online)
  • Jabaws: multiple sequence alignment with Clustal Omega, Clustal W, MAFFT, MUSCLE, T-Coffee, ProbCons, MSAProbs, and GLProbs; prediction of protein disorder with DisEMBL, IUPred, Jronn, GlobPlot; calculation of amino acid alignment conservation with AACon (online and standalone)
  • PredictProtein: started out by predicting secondary structure and returning families of related proteins. Solvent accessibility and transmembrane helix prediction followed suit shortly thereafter (online)
  • PSSweb: structural statistics (online)
  • ConSurf: identification of functional regions, map conserved amino acids (online)
  • KMAD: intrinsically disordered proteins (online)
  • PSI/TM-Coffee: Align Proteins using Homology Extension against Reduced Databases (online)
  • TCS: Evaluates your Alignment and outputs a Colored version indicating the local reliability (online)
  • AlignMe (membrane proteins) (online and standalone)
  • Memoir: membrane proteins, homology modelling algorithm designed for membrane proteins. The inputs are the sequence which is to be modelled, and the 3D structure of a template membrane protein (online)
  • PconsC3 (accurate contact predictions) (online)
  • RFcon: predicting protein residue-residue contacts using random forests and deep networks (standalone and online)
  • PROMALS3D: multiple sequence and structure alignment server (online)
  • BlockLogo: input multiple seq alignment (online)
  • PRALINE: multiple sequence alignment (online)
  • Skylign: tool for creating logos representing both sequence alignments and profile hidden Markov models (generate logo) (online)
  • DIALIGN: multiple sequence alignment (online)
  • Seq2Logo: web-based sequence logo generation (online)
  • DALI 3D, sequence align, logo, service for comparing protein structures in 3D (online)
  • UniProt: protein database (online)
  • PDBsum: Pictorial database of 3D structures in the Protein Data Bank (online)
  • 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

  • Chimera: (standalone)
  • PyMolshortcuts: Shortcuts For Faster Image Creation in PyMOL - Scripts (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)
  • 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)
  • 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: (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: (online)
  • PyMol: (standalone)
  • 3D Protein Imaging: macromolecule figure generator (online)
  • OpenStructure: (standalone)
  • PLIP : view protein-ligand non covalent interactions (standalone)
  • ProteinsPlus: prepare and analyze protein and ligands (online)
  • PLIP: protein-ligand non covalent interactions (online)
  • SAMSON: software for adaptative modeling and simulation (nano), GROMACS can be launched from SAMSON... (standalone)
  • ProteinVolume: calculating molecular van der Waals and void volumes in proteins (online)
  • VADAR: Volume, Area, Dihedral Angle Reporter.. is a compilation of more than 15 different algorithms and programs for analyzing and assessing peptide and protein structures from their PDB coordinate data (Ramachandran plot, surface area…) (online)
  • MoMA-LigPath: MoMA-LigPath is a web server simulating protein-ligand unbinding (online)
  • MOLEonline: provides a direct access to MOLE functionality and enables on-line and easy-to-use interactive channel analysis (online)
  • BetaCavityWeb: webserver which computes cavities for a given molecular structure and a given spherical probe, and reports their geometrical properties (online)
  • Ezmol: A wizard for protein display and image production (online)
  • QuteMol: (standalone)
  • ICM: (standalone)
  • CCP4: (standalone)
  • Swiss-PdbViewer -DeepView: (standalone)
  • cellPACK: biological software tool designed to assemble large scale models from molecular building-blocks (standalone)
  • cellVIEW: a Tool for Illustrative and Multi-Scale Rendering of Large Biomolecular Datasets (standalone)
  • Avogadro: advanced molecule editor and visualizer designed for cross-platform use (draw molecules...) (standalone)
  • MolView: draw and viewer in 2D or 3D of small molecules and proteins (online)
  • Aquaria simplifying the generation of insight from protein structures (online)
  • WebMolCS: server to visualize 3D Chemical Spaces (online and standalone)
  • Web3DMol: view protein in 3D and sequences (online)
  • RealityConvert (makes objects compatible for Augmented Reality and Virtual Reality and for 3D printing) (online and standalone)
  • VMD: molecular visualization program (standalone)

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

  • MODalign: display & check and improve alignments (online)
  • CAMEO: continuously evaluate the accuracy and reliability of predictions (online)
  • Robetta: protein structure prediction service (homology modeling and ab initio fragment assembly) (online)
  • CABS-FOLD: de novo modeling, can also use alternative templates (consensus modeling) (online)
  • DeepFR: Remote template selection, 3D modeling, ab initio (online)
  • Integrative Modeling Platform (IMP): Modeling Biological Complexes Using Integrative Modeling Platform (online)
  • ValTrendsDB: bringing Protein Data Bank validation information closer to the user (online)
  • PSICA: a fast and accurate web service for protein model quality analysis (online)
  • DaReUS-Loop: a web server to model multiple loops in homology models (online)
  • Yosshi: web-server for disulfide engineering by bioinformatic analysis of diverse protein families (biologics, online)
  • Protein Folding via deep learning: End-to-End Differentiable Learning of Protein Structure (standalone)
  • IntFOLD: unified resource for the automated prediction of: protein tertiary structures with built-in estimates of model accuracy (EMA), protein structural domain boundaries, natively unstructured or disordered regions in proteins, and protein-ligand interactions (online)
  • VoroMQA: assessing three-dimensional structures of proteins and protein complexes (online)
  • INGA 2.0: improving protein function prediction for the dark proteome (can process entire genomes) (online)
  • GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein model structure (online)
  • KORP: Knowledge-based 6D potential for fast protein and loop modeling (online)
  • Ornate: Protein model quality assessment using 3D oriented convolutional neural networks (standalone)
  • TOPOLINK: A package to evaluate structural models using chemical crosslinking distance constraints (standalone and online)
  • HMMER: biosequence analysis using profile hidden Markov models (standalone)
  • HMMER: (online)
  • TCRmodel: high resolution modeling of T cell receptors from sequence (online)
  • GapRepairer: server to model a structural gap and validate it using topological analysis (loop, linker...) (online)
  • Mustguseal: Multiple Structure-Guided Sequence Alignment of Protein Families (online)
  • PREFMD: protein structure refinement via molecular dynamics simulations. Standalone scripts also available (online)
  • SuperLooper2: insertion of missing segments such as loops in proteins (SL2) (online)
  • SwissModel: fully automated protein structure homology-modelling server (online)
  • I-TASSER: (Iterative Threading ASSEmbly Refinement) is a hierarchical approach to protein structure and function prediction. It first identifies structural templates from the PDB by multiple threading approach LOMETS, with full-length atomic models constructed by iterative template fragment assembly simulations (online)
  • HHpred: homology and structure prediction (online)
  • ModWeb: A Server for Protein Structure Modeling, Sali's lab (online)
  • EVfold: uses evolutionary variation. Explore a set of ranked predicted 3D structure models (online)
  • PyMod: homology modeling with PyMOL possible (standalone)
  • 3D-DART: a DNA structure modelling server (online)
  • ORION: sensivitve method for protein template detection (Optimized protein fold RecognitION) (online)
  • Phyre2: Protein Homology/analogY Recognition Engine (online)
  • SPARKSX: fold recognition (online)
  • ESyPred3D: automated homology modeling program (online)
  • QUARK ab initio protein folding (online)
  • MEMOIR membrane protein modeling (online)
  • (PS)2-v2: Protein Structure Prediction Server (online)
  • RaptorX: a Web Portal for Protein Structure and Function Prediction (online)
  • BHAGEERATH-H: A Homology ab-intio Hybrid Web server for Protein Tertiary Structure Prediction (online)
  • 3D-JIGSAW: protein modeling (online)
  • FUGUE: Sequence-structure homology recognition (standalone and online(
  • Protein Model Portal (PMP): gives access to various models computed by comparative modeling methods provided by different partner sites (online)
  • GENO3D: automatic modeling of proteins three-dimensional structure online)
  • LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins (template-based protein structure prediction) (online)
  • HOMCOS: HOMology modeling of COmplex Structure (online)
  • ProFold: web server for protein fold classification (online)
  • PRIMO: PRotein Interactive MOdeling (online)
  • ModPipe: a completely automated software pipeline that can calculate protein structure models for a large number of sequences with almost no manual intervention (online)
  • RaptorX-Contact Map: predicts contact map of a protein sequence without using any templates. It applies an ultra-deep learning model to predict contacts and works particularly well on proteins without many sequence homologs (online)
  • HotSPOT Wizard: design mutations
  • Selecton: Server for the Identification of Site-Specific Positive Selection & Purifying Selection (online)
  • Matras: 3D Structure Comparison (online)
  • PDBeFold: 3D Structure Comparison (online)
  • Dali: 3D Structure Comparison (online)
  • PELE: Protein Energy Landscape Exploration, Localized perturbation, Side chain sampling, Minimization (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)
  • VADAR (Validation of 3D structures) (online)
  • ProTSAV (Validation of 3D structures, meta-server) (standalone and online)
  • ModFOLD (Validation of 3D structures) (online)
  • VLDPws (Validation of 3D structures) (online)
  • PDB_REDO (Validation of 3D structures, ligands-pockets) (online)
  • ProQ2 (Validation of 3D structures) (online)
  • ProQ3 (Validation of 3D structures) (online)
  • QMEAN (Validation of 3D structures) (standalone and online)
  • Verify3D (Validation of 3D structures) (online)
  • dDFIRE (Validation of 3D structures) (online)
  • Errat (Validation of 3D structures) (online)
  • 3DBIONOTES: automatically annotate biochemical and biomedical information onto structural models. Current sources of information include post-translational modifications, genomic variations associated to diseases, short linear motifs, immune epitopes sites, disordered regions and domain families (online)
  • Bio3D-web: built on top of the Bio3D package, for the investigation of protein structure ensembles (online)
  • Molstack: visualization and analysis of electron density data (online)

Glycomics, carbohydrates and glycobiology research

  • GLYCAM-Web: 3D prediction of carbohydrates and proteins-carbohydrates (online)
  • CHARMM-GUI Glycan Modeler: Modeling and Simulation of Carbohydrates and Glycoconjugates (online)
  • DrawGlycan-SNFG & gpAnnotate: Rendering glycans and annotating glycopeptide mass spectra (standalone and online)
  • GlycoMine_Struct: Highly accurate mapping of the human N-linked and O-linked glycoproteomes (online)
  • Glycosylator: a Python framework for the rapid modeling of glycans (standalone)
  • SugarBindDB: provides information on known carbohydrate sequences to which pathogenic organisms (bacteria, toxins and viruses) specifically adhere (online)...ExPASy
  • GlyConnect: platform integrating sources of information to help characterise the molecular components of protein glycosylation...ExPASy (online)
  • ExPASy: Glycomics resources eg: SugarSketcher... (online)
  • REStLESS: Automated Translation of Glycan Sequences from Residue-Based Notation to SMILES and Atomic Coordinates (online)
  • UniLectin3D: a database of carbohydrate binding proteins (online)
  • Glycomics@ExPASy: glycoinformatics (online)
  • UniCarbKB: online information storage and search platform for glycomics, carbohydrates and glycobiology research (online)
  • dbSWEET: An Integrated Resource for SWEET Superfamily to Understand, Analyze and Predict the Function of Sugar Transporters in Prokaryotes and Eukaryotes (online)
  • Glycosciences.de: databases and bioinformatics tools for glycobiology, carbohydrates and glycomics (online)
  • Glyco3D: a portal for structural glycosciences, glycobiology, carbohydrates (online)

Antibody modeling & related

  • SAbPred: Structural Antibody Prediction Server (online)
  • Thera-SAbDab: the Therapeutic Structural Antibody Database (online)
  • AbLIFT: Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces (online)
  • PROSS: Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability (protein-stability design, seldom introduce mutation in the core..check AbLIFT for mAb) (online)
  • mCSM-AB2: Guiding Rational Antibody Design Using Graph-Based Signatures. Web server providing rapid analysis of both individual mutations or the entire binding interface to guide rational antibody affinity maturation (online)
  • ProtaBank: provides a central repository for researchers to store, query, analyze, and share all types of protein engineering data (including antibodies, mAbs). Explore the impact of protein mutations (online)
  • OptMAVEn_2.0 and HUMANIZER: tools (affinity and more humanized sequences) for antibody design (standalone)
  • abYsis: A fully integrated antibody discovery system (online)
  • ABCD database: a repository for chemically defined antibodies (online)
  • Yvis: antibody high-density alignment visualization and analysis platform with an integrated database (online)
  • AppA: analysis, comparison, and visualization of contact residues and interfacial waters of antibody-antigen structures and models (online)
  • AbPredict 2: a server for accurate and unstrained structure prediction of antibody variable domains (online)
  • AbDesigner3D: a structure-guided tool for peptide-based antibody production (online)
  • BRepertoire: a user-friendly web server for analysing antibody repertoire data (online)
  • Rosetta Antibody (online)
  • PIGSpro: automatic modeling of immunoglobulin variable domains (online)
  • SmrtMolAntibody: commercial tool
  • Tabhu: AntiBody Humanization (online)
  • PIGSPro: prediction of Ab structures (online)
  • AAgAtlas: Human autoantigens (database with their associated diseases) (online)
  • TABS: Therapeutic Antibody Database (online)
  • AnkPlex: refinement of near-native ankyrin-protein docking, protein used to replace antibodies (online)

GPCR modeling

  • GPCRdb 2018: adding GPCR structure models and ligands (online)
  • WDL-RF :Predicting Bioactivities of Ligand Molecules Acting with G Protein-coupled Receptors by Combining Weighted Deep Learning and Random Forest (online)
  • GPCRmd: comprehensive database and web platform for MD simulations of GPCRs and related analysis including dataviz (online)
  • GPCR-SSFE :fragment-based molecular modeling web tool for Class A G-protein coupled receptors (online)
  • GPCR-SSFE: including Snake-like-Plot for GPCRs (online)
  • Galaxy7TM :flexible GPCR-ligand docking by structure refinement (improves an input GPCR structure by simultaneous ligand docking and flexible structure refinement using GALAXY methods) (online)
  • GPCR-ModSim :A comprehensive web based solution for modeling G-protein coupled receptors (online)
  • ModRefiner :algorithm for atomic-level, high-resolution protein structure refinement (online)
  • GPCRM: A web service to predict structures of G-protein-coupled receptors (GPCRs) using advanced homology modeling tools (online)
  • GPCR-I-TASSER: computational method designed for 3D structure prediction of G protein-coupled receptors (online)
  • GPCRautomodel: Automatic Modeling of G-Protein Coupled Receptors based on Fold Recognition Techniques: Application to Mammalian Olfactory Receptors (online)
  • GOMoDo: A GPCRs Online Modeling and Docking Webserver (online)

Protein-protein docking

  • pyDock : structural prediction of protein-protein interactions (online)
  • IRaPPA: pyDockRescoring Server (online)
  • PRODIGY-crystal: classification of biological interfaces in protein complexes (online)
  • HawkDock: to predict and analyze the protein-protein complex based on computational docking and MM/GBSA (online)
  • CoDockPP: A Multistage Approach for Global and Site-Specific Protein-Protein Docking (online)
  • InterPred: A pipeline to identify and model protein-protein interactions (online)
  • GalaxyTongDock: Symmetric and asymmetric ab initio protein-protein docking web server with improved energy parameters (online)
  • ezCADD: a Rapid 2D/3D Visualization Enabled Web Modeling Environment for Democratizing Computer-Aided Drug Design (small molecule docking, protein docking, 2D/3D interaction viz, de novo lead optimization, pocket search and polypharmacology) online
  • ClusPro FMFT-SAXS: Ultra-fast Filtering Using Small-Angle X-ray Scattering Data in Protein Docking (online and standalone)
  • RosettaDock: Efficient Flexible Backbone Protein-Protein Docking for Challenging Targets (standalone and online)
  • QASDOM: Quality ASsessment of DOcking Models, protein-protein (online)
  • DockQ: A Quality Measure for Protein-Protein Docking Models (standalone)
  • Dockground: A comprehensive data resource for modeling of protein complexes, datasets, decoys... (online)
  • LightDock: a new multi-scale approach to protein-protein docking (standalone)
  • (PS)2: Protein Structure Prediction Server (can be used for complexes) (online)
  • Memdock: alpha-helical membrane protein docking algorithm (online)
  • DOCKSCORE: rank docked poses (online)
  • DockStar: Modelling of multimolecular protein complexes (online)
  • FiltRest3D: filter predicted models (online)
  • InterEvDock2: protein docking using evolutionary and biological information from homology models and multimeric inputs (online)
  • webSDA: Simulation of Diffusional Assosiation (SDA) (online)
  • AIDA: Ab Initio Domain Assembly Server (online)
  • FiberDock, FireDock, FlexDock, PatchDock (online)...
  • FRODOCK: Fast Rotational DOCKing (online)
  • DOCK/PIERR: Protein Docking Server (online)
  • ZDOCK: docking (online)
  • PRISM: PRotein Interactions by Structural Matching (online)
  • SwarmDock: webservice for generating 3D structures of protein-protein complexes (online)
  • 3D-Garden: A system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm (online)
  • GRAMM-X: Protein-Protein Docking Web Server (online)
  • Haddock: High Ambiguity Driven protein-protein DOCKing (online requires login)
  • Cluspro: protein docking (online)
  • ClusPro-DC: discrimination between Xray and biological dimers (online requires login)
  • DisVis: visualizes the accessible interaction space (online)
  • GalaxyRefineComplex: Protein-protein complex structures generated by protein-protein docking methods can be refined (online)
  • PRODIGY: PROtein binDIng enerGY prediction (online)
  • Arpeggio: A webserver for calculating interatomic interactions in protein structures (online & standalone, server could be down)
  • 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 (online)

Protein-protein pairwise prediction & networks, pathways

  • I2D: Integrated Interactions Database is the first database providing tissue-specific protein-protein interactions (PPIs) for model organisms and human (online)
  • CyTargetLinker: Extend biological networks (eg disease network with Chembl or drugbank compounds) in Cytoscape (standalone)
  • DOMMINO 2.0: a structural Database Of Macro-Molecular INteractiOns (online)
  • ProtDCal-Suite: numerical codification and functional analysis of proteins. Set of machine learning-based methods for studying proteins, PPI-Detect for PPI and protein-peptides... (online)
  • The OncoPPi Portal: an integrative resource to explore and prioritize protein-protein interactions for cancer target discovery (online)
  • Intersppiv2: A machine learning-based predictor of human-bacteria protein-protein interactions by incorporating comprehensive host network properties (online)
  • PPI disease pathways: Large-scale analysis of disease pathways in the human interactome (datasets, standalone, also available at marinkaz / pathways on GitHub)
  • Interactome INSIDER: a structural interactome browser for genomic studies, look at mutations (via HGMD, ClinVar, COSMIC) (online and standalone)
  • MEGADOCK-Web: an integrated database of high-throughput structure-based predicted protein-protein complexes (online)
  • HPID: human protein interaction database (online)
  • WebPropagate: a web-server for network propagation on PPI networks (online)
  • BIANA: Biologic Interaction and Network Analysis (standalone)
  • BIPS: Biana Interolog Prediction Server (online)
  • BioGRID: Biological General Repository for Interaction Datasets (online)
  • Consensuspathdb: integrates interaction networks in Homo sapiens including binary and complex protein-protein, genetic, metabolic, signaling, gene regulatory and drug-target interactions, as well as biochemical pathways (online)
  • Complex Portal: a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms (online)
  • LENS: Enrichment and network studies of proteins (online)
  • DT-Web: DT-Web: a web-based application for drug-target interaction and drug combination prediction through domain-tuned network-based inference (periodically synchronized with DrugBank and PathwayCommons) (online)
  • PPI3D: search, analyze and model protein-protein interactions in the context of 3D structures (online)
  • PluriPred: web server for predicting proteins responsible for pluripotency (online)
  • Deathbase: Cell Death Processes and Pathways (online)
  • ApoCanD: Database of Human Apoptotic Proteins in the context of cancer
  • PROFEAT: computing commonly used proteins features from amino acid sequence, and interaction network properties from network structure (online)
  • PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data (online)
  • HIPPIE: web tool to generate reliable and meaningful human protein-protein interaction networks (online)

Protein-protein binding region predictions and analysis

  • PROFisis: machine learning-based method that identifies interacting residues from sequence alone (online)
  • MAPPIS: Multiple Alignment of Protein-Protein InterfaceS (PPIs) (online)
  • PCRPi: Integrates diverse metrics into a unique probabilistic measure (online)
  • HotRegion: Predicts hot regions (online)
  • HotPoint: Hotspot Prediction Server For Protein Interfaces (online)
  • FOLDEF: Uses FoldX energies to predict the hot spot residues (online)
  • MutaBind: evaluates the effects of variations and disease mutations on protein-protein interactions only for soluble complexes (online)
  • Piface: A Clustered Protein-Protein Interface Database (online)
  • ProtCID: Protein Common Interfaces Database (online)
  • Patch-DCA: Improved Protein Interface Prediction by utilizing Structural Information and Clustering DCA scores (standalone)
  • PAIRPred: Partner Aware Interacting Residue PREDictor (standalone)
  • PPISP: Protein-protein interaction site prediction through combining local and global features with deep neural networks (online and standalone)
  • SCRIBER: accurate and partner type-specific prediction of protein-binding residues from proteins sequences (online)
  • IDRBind: protein interface predictor for binding sites of intrinsically disordered protein regions (IDRs), ranging from peptide motifs (i.e., short linear motifs) to molecular recognition features (MoRFs) (online)
  • PRODIGY-crystal: classification of biological interfaces in protein complexes (online)
  • SeRenDIP: SEquential REmasteriNg to DerIve Profiles for fast and accurate predictions of PPI interface positions, sequence-based (online, standalone and datasets)
  • PIZSA: an empirical scoring scheme for evaluation of protein-protein interactions (online)
  • 3DPatch: fast 3D structure visualization with residue conservation (online)
  • MoRFpred: Predicting Functions of Disordered Proteins, input sequence (online)
  • BIPSPI: a method for the prediction of Partner-Specific Protein-Protein Interfaces. BIPSPI employs Extreme Gradient Boosting (XGBoost) models trained on the residue pairs of the protein complexes, input sequences or PDB (online)
  • ArDock: Identification and visualization of protein binding regions. Arbitrary docking can reveal potential interaction sites on the surface of a protein using docking with a set of 25 random protein probes (online)
  • ComplexContact: inter-protein contact prediction using deep learning (RaptorX-contact, input sequences, online)
  • DIBS: a repository of disordered binding sites mediating interactions with ordered proteins - database (online)
  • iPred scans the surface of a protein structure and identifies potential hotspots, input PDB (online)
  • IChemPIC Random forest classifier of biological and crystallographic protein-protein interfaces, input PDB (online)
  • SpotOn: Identification of Protein-Protein Interface Hot-Spots, requires PDB as input (online)
  • metaPPI: meta approach to predict protein-protein interaction binding site, input PDB (online)
  • meta-PPISP: a meta web server for protein-protein interaction site prediction (online)
  • PresCont: tools to predict interface residues input PDB, seq alignment, many other tools to predict structurally important residues (CLIPS-1D), residues important for protein function (H2r), generation of consensus seq logo (cSeqLogo) online
  • Cons-PPISP: consensus neural network method for predicting protein-protein interaction sites, input PDB (online)
  • bindML:Predicting Protein-Protein Interaction Sites using Phylogenetic Substitution Models, input PDB and sequence alignment (online)
  • SPIDDER: Solvent accessibility based Protein-Protein Interface iDEntification and Recognition, input PDB, could also be sequences (online)
  • Patch Finder: the new version is called BindUP (BindUP: a web server for non-homology-based prediction of DNA and RNA binding proteins, including all PatchFinderPlus features), input PDB (online)
  • DNAproDB: web-based database and structural analysis tool that offers a combination of data visualization, data processing and search functionality that improves the speed and ease with which researchers can analyze, access and visualize structural data of DNA-protein complexes (online)
  • InterProSurf: predict functionally important amino acids on protein surface crucial for protein function and protein-protein interaction (many other tools, GetArea, EpiSearch to predict conformational epitopes...) online
  • Pred_PPI: Based on auto covariance (AC) and support vector machine (SVM), this tool is capable of predicting PPIs for any target protein pair only using their primary sequences (online)
  • PredUs: uses structural information to predict what residues on protein surfaces are likely to participate in complexes with other proteins, input PDB (online)
  • iFraG: a protein-protein binding site prediction server based on common minimal sequence fragments with known interacting protein pairs, input sequences (online)
  • PSC: Protein Surface Classification by the spatial patterns of functional surfaces: insights into the binding sites, molecular functions and structural evolution (online)
  • The database JET2 Viewer (putative protein binding sites, PPI, pocket descriptors, for all PDB structures) (online)
  • ProteinPlus: Visualize structures and create 2D pose depictions, prepare proteins for docking, add hydrogens (Protoss), predict binding pockets (DoGSiteScorer), visualize electron density (EDIA), Screening of structures based on selection criteria (StructureProfiler), Find structural data of the PDB to activity values stored in the ChEMBL database (ActivityFinder)...input PDB (online)
  • IBIS (Inferred Biomolecular Interaction Server)
  • PISA (PDBePISA, interactive tool for the exploration of macromolecular interfaces, input PDB, online)
  • EPPIC: Evolutionary Protein-Protein Interface Classifier...input PDB (online)

Protein-protein complex prediction - template-based

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

Protein-membrane (transient or not) + interaction

  • MODA: membrane optimal docking area, find membrane binding sites on a protein (online)
  • MERMAID: web server to prepare and run coarse-grained membrane protein dynamics (online)
  • PredMP: a web server for de novo prediction and visualization of membrane proteins (online)
  • EncoMPASS: Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry (online)
  • LipidBuilder: and micelle generator (online)
  • ANVIL (Assignment aNd VIsualization of the Lipid bilayer) (standalone)
  • Micelle Maker: online
  • PPM server: calculates rotational and translational positions of transmembrane and peripheral proteins in membranes using their 3D structure (PDB coordinate file) as input (online)
  • PACKMOL: creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space (standalone)
  • INSert membrANE (INSANE) - coarse grain Martini (standalone)
  • MemBuilder: standalone
  • (Pro)tein (B)ilayer (L)ipid (M)embrane (ProBLM)
  • MemProtMD (Membrane-embedded structures), database of around 3500 intrinsic membrane protein structures (online)
  • RHYTHM A Knowledge Based Prediction of Helix-Helix Contacts (online)
  • CCTOP: a Consensus Constrained (transmembrane) TOPology prediction web server (online)
  • FATSLiM: to analyze MD simulations of membranes (standalone)
  • OPM-DB (prepare protein-membrane systems) online
  • Transmembrane protein Models Positioned in the Lipid bilayer (TMPL, online)
  • Protter (interactive protein feature visualization, online)
  • Memdock (alpha-helical membrane protein docking algorithm, online)
  • TOPCONS: Consensus prediction of membrane protein topology and signal peptides (online)
  • DGpred: deltaG prediction for TM helix insertion (online)
  • Membrane Protein Explorer (MPEx: a tool for exploring the topology and other features of membrane proteins by means of hydropathy plots based upon thermodynamic and biological principles (standalone)
  • CELLmicrocosmos MembraneEditor: online and standalone

Molecular simulation - refinement - flexibility (macromolecules)

  • 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)
  • P3Fold: Fast and Flexible Coarse-grained Prediction of Protein Folding Routes using Ensemble Modelling and Evolutionary Sequence Variation (online)
  • ProDy: free and open-source Python package for protein structural dynamics analysis (standalone)
  • SignDy: Signature Dynamics of Protein Families. Calculates the signature dynamics of families of proteins that share similar folds, but not necessarily similar sequences(standalone)
  • SMOG: Structure-based Models for Biomolecules (online)
  • GOdMD: GO discrete Molecular Dynamics. Conformational Transitions with Coarse-Grained Dynamics (standalone or online)
  • FlexServ: shows in an easy and visual way flexibility-related properties of proteins (online)
  • UNRES: study protein folding by molecular simulations, coarse grain (standalone)
  • UNRES server: ab initio simulations of protein structure and dynamics by using the coarse-grained UNRES model (online)
  • PRS: Perturbation Response Scanning. PRS calculates the effectiveness and sensitivity of residues in propagating allosteric signals (standalone)
  • coMD: hybrid method with a VMD plugin designed for efficient simulations of conformational changes (standalone)
  • BitClust: Fast and memory efficient clustering of long Molecular Dynamics (standalone)
  • ENCoM: coarse-grained normal mode analysis method (can be used to investigate mutations) (standalone)
  • MDAnalysis: a toolkit for the analysis of molecular dynamics simulations (standalone python)
  • MDsrv: viewing and sharing molecular dynamics simulations on the web (online)
  • Tios: The Internet of Simulations. Turning Molecular Dynamics into a Data Streaming Web Application (standalone)
  • KBbox: A Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding (online advices for tool selection)
  • DDT: Drug Discovery Tool, a fast and intuitive graphics user interface for Docking (autodock) and Molecular Dynamics analysis (standalone)
  • GPathFinder: extension built over GaudiMM core to allow the identification of ligand binding pathways at atomistic level (standalone)
  • MERMAID: web server to prepare and run coarse-grained membrane protein dynamics (online)
  • PyRod: Tracing water molecules in molecular dynamics simulations to predict hotspots and binding pockets (standalone)
  • SNP2SIM: a modular workflow for standardizing molecular simulation and functional analysis of protein variants (standalone)
  • Kinact: a computational approach for predicting activating missense mutations in protein kinases (online)
  • SAMSON: ligand unbinding pathways (standalone)
  • Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Polarizable Force Fields
  • CABS-flex: a simulation environment for fast modeling of protein flexibility (standalone)
  • gRINN :a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations
  • MODE-TASK Large-scale protein motion tools
  • CABS-flex :fast simulations of flexibility of protein structures
  • Pyrite: A blender plugin for visualizing molecular dynamics simulations using industry-standard rendering techniques
  • Scoria: a Python module for manipulating 3D molecular data
  • HullRad Fast Calculations of Folded and Disordered Protein and Nucleic Acid Hydrodynamic Properties
  • STOCK: The structure mapping tool allows one to map an atomistic representation of a single molecule to a coarse-grained representation. The end result is a topology and weights mapping XML file as is used in VOTCA or DL CGMAP coarse-graining simulation packages (online)
  • DynaMine Fast predictor of protein backbone dynamics using only sequence information as input
  • QwikMD MD with VMD and NAMD (standalone Mac, Linux, Windows, Supercomputers)
  • WEBnm@ Web server and services for comparing protein flexibility
  • NMSim integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins
  • FoldX (simulation, Alascan, mutation, peptides...loops)
  • FoldX 5.0: Working with RNA, small molecules and a new graphical interface (standalone)
  • Naccess: calculates the accessible area of a molecule from a PDB file
  • FreeSASA: calculates the accessible area of molecules, different chains, etc
  • dr_SASA: Calculation of accurate interatomic contact surface areas for the quantitative analysis of non-bonded molecular interactions (online and standalone multiple OS)
  • ProteinPrepare Make your protein ready for molecular dynamics simulations by titrating and protonating the protein at a desired pH and by optimizing the H-bond network
  • Adaptativesampling Explore the protein conformational space or protein-ligand interaction space by running MD simulations along the metric of your choice
  • PREFMD: protein structure refinement via molecular dynamics simulations (Online and Standalone scripts also available)
  • Abalone: Molecular simulations with AMBER-ii force field, Molecular Dynamics folding
  • AQUASOL predict water binding sites
  • DRoP: Automated detection of conserved solvent binding sites on proteins (online with login and standalone)
  • VLDP tool for analysing protein structures based on Laguerre diagram, can also be used to add water online
  • PreFRP: Prediction and visualization of fluctuation residues in protein structure (online)
  • 3Drefine: protein structure refinement server (online)
  • ModRefiner: atomic-level, high-resolution protein structure refinement (online)
  • FG-MD: molecular dynamics (MD) based algorithm for atomic-level protein structure refinement (online)
  • NOMAD-ref: Normal mode calculation and visualisation (online)
  • iMODS: explore the colletive motions of proteins and nucleic acids using NMA in internal coordinates (torsional space) (online)
  • WEBnma: Web-server for Normal Mode Analysis of proteins (online)
  • MDWeb: personal workspace providing standard protocols to prepare structures, run standard molecular dynamics simulations and to analyze trajectories (online)
  • Gromacs: via the WeNMR suite for Structural Biology (online)
  • AMBER: suite of biomolecular simulation programs (standalone)
  • CHARMM: Chemistry at HARvard Macromolecular Mechanics (standalone)
  • CHARMM-GUI (eg solvator to add water molecules...)
  • DynOmics (dynamics of structural proteome) (online)
  • Amber tools: a suite of biomolecular simulation programs (standalone)
  • SEBOMD: Semi-Empirical Born–Oppenheimer Molecular Dynamics (SEBOMD) within the Amber Biomolecular Package (standalone)
  • YASARA: molecular-graphics, -modeling and -simulation program (standalone)
  • GROMITA-GUI: Graphical User Interface (GUI) front-end for the molecular sumulation package, GROMACS (standalone)
  • Gromacs: molecular simulation (standalone)
  • WnS: Systematic exploration of multiple drug binding sites, Wrap 'n' Shake (WnS) (combine AutoDock 4.2.3 and GROMACS) (standalone)
  • FireProt: automated design of thermostable proteins (online)
  • SEEKR: scripts for ligand-receptor kinetic calculations (standalone)
  • NWChem: High-Performance Computational Chemistry (standalone)
  • MCTBI: metal ion effects in RNA structures (online)
  • SimRNAweb: simulation RNA (online)
  • 3D-NuS: simulation non-canonical 3-Dimensional Nucleic Acid Structures (online)
  • CHARMM-GUI: provides a web-based graphical user interface to generate various molecular simulation systems and input files (online)
  • FlexPred: Protein fluctuation prediction using SVR (online)
  • SPECTRUS: performs a decomposition into quasi-rigid domains of proteins or protein complexes, based on the analysis of the distance fluctuations between pairs of amino acids (online)
  • Bio3D-web NMA: normal mode analysis of protein structures (elastic network models (ENMs), residue fluctuations, mode visualization...(online)
  • LipidBuilder: online
  • HTMD: a molecular-specific programmable environment to prepare, handle, simulate, visualize and analyze molecular systems (standalone)

Electrostatics of macromolecules (mainly)

  • Bluues: Electrostatic properties of proteins based on generalized Born radii (online)
  • DFMD: Fast and Effective DelPhiForce Steered Molecular Dynamics Approach to Model Ligand Approach Toward a Receptor (standalone)
  • PKAD: a database of experimentally measured pKa values of ionizable groups in proteins (online database)
  • APBS and PDB2PQR: electrostatic and solvation properties for complex molecules (online and standalone)
  • ProteinPrepare Make your protein ready for molecular dynamics simulations by titrating and protonating the protein at a desired pH and by optimizing the H-bond network (online)
  • Protein-Sol: Web-based display of protein surface and pH-dependent properties for assessing the developability of biotherapeutics (with 3D data) (online)
  • TKSA-MC: A Web Server for rational mutation through the optimization of protein charge interactions (Tanford-Kirkwood Surface Accessibility model) (standalone on GitHub) (online)
  • PBEQ Solver: calculates and visualizes the electrostatic potential of a molecule by solving the Poisson-Boltzmann (PB) equation (online)
  • PCE: Protein Continuum Electrostatics (electrostatic potentials and pKa) (online)
  • H++: automated system that computes pK values of ionizable groups in macromolecules and adds missing hydrogen atoms according to the specified pH of the environment (online)
  • DelPhiPKa: protonation and pKa calculation (online)
  • DelPhiForce: electrostatic forces and energy calculations and visualization between two objects (online)
  • ESBRI Evaluating the Salt BRIdges in Proteins (online)
  • SMPBS: size Modified Poisson-Boltzmann Solvers (online)
  • PDBparam: check salt-bridges, cation-pi, etc (online)

Ligand-binding pockets

  • Erebus: Protein rigid substructure search (online, requires login)
  • D3Pockets: A Method and Web Server for Systematic Analysis of Protein Pocket Dynamics (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-Dock: a web server for cavity detection-guided protein-ligand blind docking (online)
  • LPIcom: web server developed for understanding protein-ligand interaction for almost all ligands available in Protein Data Bank (online)
  • DRoP: Automated detection of conserved solvent binding sites on proteins (online with login and standalone)
  • PatchSearch: a web server for off-target protein identification (input a protein complexed with a ligand and identifies within user-defined or predefined collections of protein structures, those having a binding site compatible with this ligand in terms of geometry and physicochemical properties) (online)
  • Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport (built on top Caver 3.02 and CaverDock 1.0) (online)
  • PrankWeb: a web server for ligand binding site prediction and visualization. Users can utilize the server API directly, bypassing the need for a web-based frontend or installation of the P2Rank application (online)
  • Drug ReposER: web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning (pocket comparison, ligand transposition) (online)
  • DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network (standalone)
  • CASBench: A Benchmarking Set of Proteins with Annotated Catalytic and Allosteric Sites in Their Structures (online database test pocket tools or docking)
  • PyRod: Tracing water molecules in molecular dynamics simulations to predict hotspots and binding pockets (standalone)
  • ProSPECCTs: A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets
  • PPD: Protein pocket detection via convex hull surface evolution and associated Reeb graph (online & standalone in C)
  • PYWINDOW: Python package for the analysis of structural properties of molecular pores (standalone)
  • P2RANK: novel machine learning-based method for prediction of ligand binding sites from protein structure. P2RANK uses Random Forests classifier to infer ligandability of local chemical neighborhoods near the protein surface which are represented by specific near-surface points and described by aggregating physico-chemical features projected on those points from neighboring protein atoms (standalone)
  • ezCADD: a Rapid 2D/3D Visualization Enabled Web Modeling Environment for Democratizing Computer-Aided Drug Design (small molecule docking, protein docking, 2D/3D interaction viz, de novo lead optimization, pocket search and polypharmacology) online
  • 3DLigandSite : CNIO, predict binding pocket with or without 3D structure of the target (online)
  • COACH-D :improved protein–ligand binding sites prediction with refined ligand-binding poses through molecular docking (online)
  • CASTp 3.0 :computed atlas of surface topography of proteins (output can be investigated via Chimera or Pymol) (online)
  • CAVER Analyst 2.0 (Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories (standalone Windows))
  • CavityPlus : Predict CavPharmer (receptor-based pharmacophore modelling), CorrSite (allosteric ligand-binding sites), and CovCys (druggable cysteine residues) (online)
  • AlloFinder :a strategy for allosteric modulator discovery and allosterome analyses (not for pocket but ligand) (online)
  • BINANA: (BINding ANAlyzer) python tool for analyzing ligand-target interactions (Hbonds, cation-Pi, etc, standalone for linux boxes, may work on Mac), if URL not working, seems to be at GitHub
  • Cryptoscout Predict cryptic sites and druggable cavities on a protein structure using mixed-solvent molecular dynamics simulations in presence of benzene (online)
  • APoc: large-scale identification of similar protein pockets (standalone)
  • PESDserv: Allows high-throughput protein binding site comparison (online)
  • SiteEngine: Predicts regions that can potentially function as binding sites (recognition of geometrical and physico-chemical environments that are similar to known binding sites) (online and standalone)
  • metaPocket 2: meta-method, Fpocket, GHECOM, ConCavity and POCASA (online)
  • EDTSurf: (pocket, surface, pocket depth...) (standalone)
  • The database JET2 Viewer: (putative protein binding sites, PPI, pocket descriptors, for all PDB structures) (online)
  • MoMA-LigPath: Molecular Motion Algorithms (MoMA). Starting from the model of a protein-ligand complex, MoMA-LigPath computes the ligand exit path from the active site to the protein surface using robotics-inspired algorithms (online, requires login)
  • BSpred: a neural network based algorithm for predicting binding site of proteins from amino acid sequences (online)
  • ASCONA: a fully automated command line tool for generating sequence alignments and superpositions of protein binding sites (standalone)
  • ISMBLab-Lig: predict binding sites for various types of ligands including ions. Tolerates 3D uncertainties (online)
  • COACH: meta-method (COFACTOR, FINDSITE and ConCavity...) (online)
  • TRAPP : a tool for analysis of transient binding pockets in proteins (online)
  • DrugEBIlity: search for pockets with as input a protein, or a ligand...provides druggability scores (online)
  • AlloSite: allosteric site (online)
  • Screen2: geometry-based (online)
  • SiteHound-web: energy-based (send chemical probes) (online)
  • SiteComp: pocket comparison (online)
  • SiMMap: Provides the graphic visualization of the site-moiety map and anchors elements, including a binding pocket with interacting residues, requires ligand (online)
  • ConCavity: prediction from protein sequence and structure (geometry-based) (online)
  • SplitPocket: geometry-based (online)
  • Pepsite2: Prediction of peptide binding sites on protein surfaces (online)
  • POCASA: geometry-based, pockets and cavities, volume... (online)
  • MolAxis: accurate Identification of Channels in Macromolecules (online)
  • MultiBind Multiple Alignment of Protein Binding Sites: pocket comparison (online)
  • SiteEngines: Functional Sites Structural Search Engine (online)
  • 3D-SURFER (pocket comparison online)
  • G-LoSA: Graph-based Local Structure Alignment - Pocket alignment (standalone)
  • GalaxyWeb: predict binding site (online)
  • FTMAP: energy-based (online requires login)
  • PocketAnnotate (align pockets, comparison) (online)
  • ProBiS-ligands: can transposes ligands to the query protein, pocket comparison (online)
  • DoGSiteScorer: druggability score (online)
  • PocketQuery: energy-based (online)
  • FPOCKET: mainly geometry-based (online)
  • Hpocket: (online)
  • MDpocket: (online)
  • Nucleos: identification of nucleotide-binding sites (online)
  • ACTIVE SITE PREDICTION: compute cavities (online)
  • GHECOM (geometry-based): finding multi-scale pockets on protein surfaces using mathematical morphology (online)
  • Patchsurfer (pocket comparison online)
  • Patch-Surfer 2 (predicts binding ligands, pocket comparison online)
  • SPACER: Predicting Allosteric site (online)
  • iDrug: (online)
  • pocketZebra: Selection and Classification of Subfamily-Specific Binding Sites by Bioinformatic Analysis Of Diverse Protein Families (online)
  • Rbpmap: a web server for mapping binding sites of RNA-binding proteins (online)
  • ProBiS: align pocket (online)
  • ProbisLigands (Predict Ligands by Similarity in Binding Sites - online)
  • FunFOLD: binding site from sequence (online)
  • IBIS: IBIS reports protein-protein, protein-small molecule, protein nucleic acids and protein-ion interactions observed in experimentally-determined structural biological assemblies (online)
  • PocketDepth: geometry-based (online)
  • DEPTH (online)
  • LigDig (online)
  • PockDrug: predict on holo and apo (online)
  • AlloPred: allosteric site (online)
  • ProBiS-CHARMMing: (online)
  • CryptoSite: flexibility, Cryptic Binding Sites (online)
  • DrugMiner: potential druggable proteins from sequence (online)
  • canSAR: (online)
  • PLIC: Clusters of similar binding sites in the PDB and analysis of various type of interactions within the clusters (online and standalone)
  • PoSSuM (pocket comparison online)
  • CatSId (pocket comparison online)
  • COFACTOR (pocket comparison online)
  • eF-seek (pocket comparison online)
  • Evolutionary Trace Annotation (ETA) (pocket comparison online)
  • fPOP (pocket comparison online)
  • Imaaagine (pocket comparison online)
  • LabelHash (pocket comparison online)
  • PDBSITE / PDBsitescan (pocket comparison online)
  • pevoSOAR (pocket comparison online)
  • PINTS (pocket comparison online)
  • PocketMatch (pocket comparison online)
  • SeSAW (pocket comparison online)
  • SPRITE (pocket comparison online)
  • SuMo (pocket comparison online)
  • TM-align (pocket comparison online)
  • HOMCOS (analyze interactions) (online)
  • ProteinPlus (structural analysis pockets...): (online)
  • IonCom (ion & small ligands) (online)
  • PARS (allosteric pockets) (online)
  • DruGUI: Druggability Analysis (standalone for VMD)
  • Geomfinder (pocket comparison): (online)
  • AutoSite: (standalone)
  • VLDPws (analyze surface & solvate - water) (online)
  • PROPORES (Novel toolkit for identifying pockets, cavities and channels of protein structures) (standalone)
  • EPOS_BP BALLPass (standalone)
  • mutLBSgeneDB mutated binding pockets, database (online)
  • PatchSearch (compare pockets) (standalone)
  • WaterDock-2.0 (PyMol) (standalone)
  • WaterDock-2.0 (standalone)
  • WATsite2.0 (water Pymol plugin)
  • PLImap (fragment mapping) (standalone Astex)
  • LIBRAWA: binding site (online)
  • LIBRA+: binding site (standalone)
  • DeepSite (binding pocket predictor, neural networks) (online)
  • IBIS (Inferred Biomolecular Interaction Server) (online)
  • omiXcore: prediction of protein-RNA interactions (online)
  • IChem (Toolkit for detecting, comparing and predicting protein-ligand interactions) (standalone)
  • STarMir (miRNA binding sites on a target mRNA) (online)
  • ChannelsDB : database for the positions, geometry and physicochemical properties of channels (pores and tunnels) found within biomacromolecular structures (eg, in CYP or membrane proteins...) (online)
  • LigQ: a Webserver to Select and Prepare Ligands for Virtual Screening (online)

Biostructural pathology / Structural analysis

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

Variation - mutation databases

  • COSMIC, COSMIC-3D...: Catalogue Of Somatic Mutations In Cancer
  • SwissVar: portal to search variants in Swiss-Prot entries of the UniProt Knowledgebase (UniProtKB) (online)
  • dbDSM: a manually curated database for deleterious synonymous mutations (single nucleotide mutation which replaces one base to another in the coding sequence that does not alter amino acids in the translated protein due to the degeneracy genetic code, affecting transcript splicing, mRNA stability, RNA secondary structure, the biding site of transcription factor binding and microRNA) (online)
  • CAGI Workshop: Assessing the future of genome interpretation (datasets)
  • GRASP: Genome-wide Repository of Associations between SNPs and Phenotypes (datasets)
  • dbVar: NCBI's database of human genomic structural variation — insertions, deletions, duplications, inversions, mobile elements, translocations, and others (database online)
  • OMIM: Online Mendelian Inheritance in Man (database online)
  • dbSNP: contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations (database online)
  • TCGA: Cancer Genome Atlas (database online)
  • HumDiv/HumVar: Human Disease Variants (database online)
  • The Genome Aggregation Database (gnomAD): aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects (database online)
  • Kaviar: Known VARiants (database online)
  • SKEMPI: Database of binding free energy changes upon mutation (database online)
  • ProNit: Database of thermodynamic data for protein-nucleic acid interactions (database online)
  • ProTherm: Database of thermodynamic data for protein stability (database online)
  • mutLBSgeneDB: Mutated ligand binding site gene DataBase (database online)
  • Platinum: Database of experimentally measured effects of mutations on structurally defined protein–ligand complexes (database online)
  • VariBench: benchmark database for variations (database online)
  • VariSNP: a benchmark database for variations from dbSNP (database online)
  • ANNOVAR: List of variant dbs & tools (database online)
  • CanProVar to store and display single amino acid alterations including both germline and somatic variations in the human proteome
  • 3DBIONOTES v3.0: Crossing molecular and structural biology data with genomic variations (online)
  • AWESOME: a database of SNPs that affect protein post-translational modifications (online)
  • AlloMAPS: allosteric mutation analysis and polymorphism of signaling database (online)
  • ActiveDriverDB human disease mutations and genome variation in post-translational modification sites of proteins
  • HPA human protein atlas - cancer and pathology…
  • Mouse Phenome Database : an integrative database and analysis suite for curated empirical phenotype data from laboratory mice
  • MSV3d missense mutations in 3D, human proteome
  • mutation3D functional prediction and visualization for aa substitutions on protein models and structures
  • Aquaria simplifying the generation of insight from protein structures
  • dbGaP
  • dbNSFP
  • ClinVar aggregates information about genomic variation and its relationship to human health (database online)
  • Database of Genomic Structural variation
  • European Genome-phenome Private variation
  • European Variation Archive (EVA) Public variation
  • The Human Genetic Variation Archive (HGVA)
  • Ensembl (a genome browser )
  • HGMD Disease-related gene lesions
  • HGVD Japanese genetic variation
  • Human Mutation Analysis HUMA
  • Online Mendelian In Man OMIM Human genes and genetic disorders
  • SNPeffect Characterization and annotation of SNPs
  • SNPs3D Functional effects of nonsynonymous SNPs
  • The Cancer Genome Atlas TCGA Cancer-associated mutations
  • Uniprot Protein database
  • VnD Variation and drugs
  • PDBSWS (PDB residues & Uniprot residue position mapping)
  • PROXiMATE (a database of mutant protein-protein complex thermodynamics and kinetics)

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

  • VIPdb: Variant Impact Predictor Database. List of tools to study variants (online)
  • VAT: Variant Annotation Tool. A computational framework to functionally annotate variants in personal genomes using a cloud-computing environment (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 (online)
  • MILAMP: Multiple Instance Prediction of Amyloid Proteins (online)
  • P3Fold: Fast and Flexible Coarse-grained Prediction of Protein Folding Routes using Ensemble Modelling and Evolutionary Sequence Variation (online)
  • ProtFus: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins (online)
  • svtools: population-scale analysis of structural variation (standalone)
  • BorodaTM: Prediction of disease-associated mutations in the transmembrane regions of proteins with known 3D structure (online)
  • MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains (online)
  • Simple ClinVar: an interactive web server to explore and retrieve gene and disease variants aggregated in ClinVar database (online and standalone perl script)
  • SNP2SIM: a modular workflow for standardizing molecular simulation and functional analysis of protein variants (standalone)
  • DNAscan: personal computer compatible NGS analysis, annotation and visualisation (standalone)
  • Interactome INSIDER: a structural interactome browser for genomic studies
  • VarQ: A Tool for the Structural and Functional Analysis of Human Protein Variants (online)
  • TKSA-MC: A Web Server for rational mutation through the optimization of protein charge interactions (Tanford-Kirkwood Surface Accessibility model) (standalone on GitHub)
  • AIMMS: a web server dedicated for prediction of drug resistance on protein mutation (online)
  • MolArt: MOLecular STructure AnnotatoR, enables users to view annotated protein sequence (including variation data from large scale studies) and overlay the annotations over a corresponding experimental or predicted protein structure
  • VarAFT: disease-causing variants annotation
  • ELASPIC: proteome-wide structure-based prediction of mutation effects on protein stability and binding affinity (online)
  • MoRFpred: Predicting Functions of Disordered Proteins (online)
  • shiny-pred: a server for the prediction of protein disordered regions (online)
  • GDA :a web-based tool for Genomics and Drugs integrated analysis
  • SNPnexus :assessing the functional relevance of genetic variation to facilitate the promise of precision medicine
  • RFAmyloid: Server for Predicting Amyloid Proteins
  • DynaMut :predicting the impact of mutations on protein conformation, flexibility and stability
  • IMPACT : oncology database integrating molecular profiles with actionable therapeutics
  • KRDS a web server for evaluating drug resistance mutations in kinases by molecular docking
  • Variant Effect Predictor (VEP) VEP (Ensembl) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions
  • G2S A web-service for annotating genomic variants on 3D protein structures
  • Disulfide by Design 2.0 (DD2) (a web-based tool for disulfide engineering in proteins)
  • TANGO A computer algorithm for prediction of aggregating regions in unfolded polypeptide chains
  • FireProt: automated design of thermostable proteins
  • ADEPTUS discovery and analysis tool based on expression and mutation data from many diseases (eg., cancer)
  • Zebra a web server for bioinformatic analysis of diverse protein families
  • visualCMAT Helps to select and interpret correlated mutations/co-evolving residues in protein families
  • MAESTROweb :a web server for structure based protein stability prediction
  • Delta (DNA, Web-based 3D genome visualization and analysis platform)
  • pStab (Prediction of Stable Mutants (single- or multiple-point substitutions of charged residues, Unfolding Curves, Stability Maps and Protein Electrostatic Frustration)
  • Folding RaCe (method for predicting changes in protein folding rates upon point mutations (two-state folders))
  • ENTPRISE: An Algorithm for Predicting Human Disease-Associated Amino Acid Substitutions from Sequence Entropy and Predicted Protein Structures
  • 3D Hotspots: mutation hotspots in protein chains (cancer) (online)
  • BeAtMuSiC: protein-protein affinity upon mutation (online)
  • BindProfX: protein-protein affinity upon mutation (online)
  • HOPE: 3D visualization, seq. and structural features (online)
  • INPS-3D: protein stability (online)
  • KD4v: phenotypic effect (online)
  • MOKCa: mutation hotspots in protein domains (cancer) (online)
  • MultiMutate: protein stability (online)
  • MUpro: protein stability from sequence (online)
  • MutationAligner: Somatic mutation hotspots in protein domains in cancer (online)
  • SAAPdap: Single Amino Acid Polymorphism data analysis pipeline - sequence or 3D (online)
  • SDS: SDS Pharmacogenes is a score that represents the number of structural disturbances caused by an amino acid variant in a pharmacogene (online)
  • STRUM: mutant stability change (online)
  • SuSPect: phenotypic effect (online)
  • VIPUR: Variant Interpretation and Prediction Using Rosetta (standalone)
  • ws-SNP&GO3d: phenotypic effect 2D and 3D (online)
  • PDBFlex: database explores the intrinsic flexibility of protein structures by analyzing structural variations between different depositions and chains in asymmetric units of the same protein in PDB. It allows to easily identify regions and types of structural flexibility present in a protein of interest (online)
  • cBioPortal: mapping and 3D visualization - cancer genomics (online)
  • JalView: multiple seq. alignment and annotation visualization (online)
  • CADD: Combined Annotation Dependent Depletion. A tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome (sequence) (online)
  • CAROL: CAROL is a combined functional annotation score of non-synonymous coding variants. PolyPhen-2 + SIFT (standalone)
  • CHASM: CHASM (Cancer-specific High-throughput Annotation of Somatic Mutations). SNV-Box is a database of pre-computed features of all possible amino acid substitutions at every position of the annotated human exome. Users can rapidly retrieve features for a given protein amino acid substitution for use in machine learning (standalone)
  • Evolutionary Action: A formal perturbation equation between genotype and phenotype determines the evolutionary action of protein coding variations on fitness (online)
  • iFish2: Integrated transcript/gene/gene-family customized classifiers for Functional Inference of non-synonymous SNVs in Human genome together with genetic data fusion (online)
  • MutPred-LOF: Frameshift and nonsense mutation pathogenicity and effect on protein structure and function (sequence) (standalone)
  • VAAST2: Variant Annotation, Analysis and Search Tool (sequence) (online)
  • nsSNPAnalyzer (predicting disease-associated nonsynonymous single nucleotide polymorphisms)
  • MutationTaster (sequence)
  • dSysMap (Mapping of Human disease-related mutations at the systemic level, structural interactome)
  • Hotspot3d (structure)
  • PISA (PDBePISA, interactive tool for the exploration of macromolecular interfaces)
  • SnpEff - SnpSift (Genetic variant annotation and effect prediction toolbox)
  • Auto-Mute 2.0 Sequence and structure based (stability change)
  • CScape : predicts oncogenic single-point mutations in the cancer genome
  • FATHMM-XF : accurate prediction of pathogenic point mutations via extended features
  • SAAFEC: An online application for calculating folding free energy changes in proteins caused by missense mutations (online)
  • DUET: stability change by combining two approaches
  • CUPSAT Structure based (stability change)
  • I-Mutant2.0 Sequence and structure based (stability change)
  • MuPro Sequence and structure based (stability change)
  • NeEMO Residue interaction networks (stability change)
  • PoPMuSiC 2.1 Structure based (stability change)
  • FATHMM Sequence based
  • MAPP Sequence based
  • Meta-SNP Consensus classifier
  • MuD Sequence and structure based
  • MutPred2 Sequence and structure-based
  • PANTHER-PSEP Sequence based
  • Parepro Sequence-based
  • PolyPhen-2 Sequence and (partially)-structure based
  • SIFT Sequence-based
  • SNAP Sequence-based
  • SNPs&GO Sequence and structure based
  • VAPOR (Variant Analysis Consensus classifier)
  • G23D
  • PredictSNP2 (consensus)
  • Cancer3D
  • MANORAA
  • mCSM-lig
  • Plot protein: visualization of mutations
  • ESBRI (salt bridges, electrostatics)
  • PROVEAN (Sequence and structure based)
  • StructMAn
  • PsychoProt
  • Pharos (druggable genome - TCRD - (target central resource database))
  • BindProf (deltadeltaG on PPI interface, needs a list of residue)
  • DrugScorePPI (deltadeltaG on PPI interface) (systematic search, hotspots)
  • PredHS (protein-protein interaction hotspots (sort of deltadelta G)
  • wANNOVAR
  • dbSNP
  • 1000 genomes project
  • mutLBSgeneDB (mutated binding pockets)
  • Genomics, Evidence, Neoplasia, Information, Exchange (GENIE)
  • MSV3d
  • DaMold
  • INPS-MD (predict stability)
  • ABCMdb (mutations in ATP binding cassette proteins - ADMET)
  • INTAA: Amino Acid Interaction (INTAA) web server. Calculation of the residue Interaction Energy Matrix for any protein structure. Aims to identify key residues within protein structures which contribute significantly to the stability of the protein (online)
  • NewProt (protein engineering portal, mutation via HOPE & the Hotspot Wizard...)
  • PON-P2 predicts the pathogenicity of aa changes
  • VEST: Variant Effect Scoring Tool
  • MuPIT: map variant positions in 3D
  • CRAVAT: cancer-related analysis of variants toolkit
  • SODA (protein solubility)
  • FELLS (fast estimator of latent local structure)
  • DEOGEN2: predictor of missense SVNs
  • MutationAssessor
  • GenProBiS (mapping variants to protein binding sites)
  • mCSM-DNA: aa changes on protein-nucleic acids
  • PhD-SNPg (coding and non-coding regions)
  • PMut
  • Prosat+ (protein structure annotation)
  • SIFTS (integrate 3D structure, function, taxonomy & sequence, PDB-UniProt mapping)
  • VCF.Filter (disease-linked genetic variants from sequencing data)
  • MAESTRO (multi agent stability prediction upon point mutations)
  • mCSM (effect of mutations on stability, PPI, protein-DNA)
  • SDM (impact of mutations on protein stability)
  • Protein-Sol (predict protein solubility from sequence)
  • Solubis (reduce protein aggregation through mutation, check for peptides)
  • Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubility (online and standalone on the way)
  • AGGRESCAN3D (A3D): prediction of aggregation (proteins)
  • Aggrescan3D: python package for structure-based prediction of protein aggregation (standalone)
  • Protter (interactive protein feature visualization)
  • Protein-Sol: Web-based display of protein surface and pH-dependent properties for assessing the developability of biotherapeutics (with 3D data) (online)
  • MutaGene (explore cancer mutations)
  • Variant Ranker (according to functional significance)
  • SCooP (protein stability curves as a function of the temperature, maybe not fully for point mutation but related)
  • MutaNET (analysis of genomic mutations in gene regulatory networks)
  • Spliceman2: predicts defects in pre-mRNA splicing

Peptide design

  • PeptiMap: Detection of peptide-binding sites on protein surfaces (online)
  • FoldamerDB: A database of peptidic foldamers, non-natural oligomers that mimic the structural behaviour of natural peptides, proteins and nucleotides by folding into a well-defined 3D conformation in solution (database online)
  • ProtDCal-Suite: numerical codification and functional analysis of proteins. Set of machine learning-based methods for studying proteins, PPI-Detect for PPI and protein-peptides... (online)
  • ELM: Eukaryotic Linear Motif (ELM) resource (online)
  • Short Peptides in SMILES: Small peptides in SMILES and three-dimensional formats for virtual screening campaigns (database)
  • SATPdb: database of structurally annotated therapeutic peptides (online)
  • Major Peptide Resources: peptide databases and tools (online)
  • PepBank: database of peptides based on sequence text mining and public peptide data sources. Only peptides that are 20 amino acids or shorter are stored (online)
  • PeptideAtlas: a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments (online)
  • WALTZ-DB 2.0: open-access database providing information on experimentally determined amyloid-forming hexapeptide sequences (online)
  • MODPEP: fast ab initio structure prediction of linear peptides or disorder proteins (online)
  • P3Fold: Fast and Flexible Coarse-grained Prediction of Protein Folding Routes using Ensemble Modelling and Evolutionary Sequence Variation (online)
  • ADCP: AutoDock CrankPep: Combining folding and docking to predict protein-peptide complexes (standalone)
  • PepVis: An integrated Peptide Virtual Screening pipeline for ensemble and flexible docking protocols (standalone)
  • PIPER-FlexPepDock: High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock (online)
  • PepX: Fast and accurate prediction of peptide docking (standalone)
  • PeptoGrid: Rescoring Function for AutoDock Vina to Identify New Bioactive Molecules from Short Peptide Libraries (standalone)
  • SPOT-peptide: Template-based prediction of peptide-binding proteins and peptide-binding sites (online)
  • SolyPep: Random peptide library generation, accounting or not for solubility, and preparing for docking (online)
  • MDockPeP: An ab-initio protein-peptide docking server (online)
  • PepBDB: a comprehensive structural database of biological peptide–protein interactions (online)
  • IEDB: Immune epitope database and analysis (online)
  • AllerTOP: Bioinformatics tool for allergenicity prediction (online)
  • HPEPDOCK :blind peptide-protein docking based on a hierarchical algorithm (online)
  • PlifePred :In silico approaches for predicting the half-life of natural and modified peptides in blood (online)
  • SPRINT-str :Structure-based Prediction of Protein-peptide Binding Regions using Random Forest (online)
  • Pep-Fold (including cyclic) (PEPFOLD) (online)
  • SPIDR :small-molecule peptide-influenced drug repurposing. SPIDR is integrated into DockoMatic v 2.1. The tool contains an intuitive graphical interface for peptide mutant screening workflow and facilitates mapping, clustering, and searching of local molecular databases. SPIDR incorporates the SimSearcher utility, which generates shape distribution signatures of molecules and employs multi-level K-means clustering to insure fast database queries (standalone)
  • Amp scanner: Deep Learning Improves Antimicrobial Peptide Recognition (Antimicrobial Peptide Scanner), online
  • FlexPepDock: a high-resolution peptide-protein docking (refinement) protocol for the modeling of peptide-protein complexes, implemented in the Rosetta framework (online)
  • MLACP: machine-learning-based prediction of anticancer peptides (online)
  • PEP-SiteFinder: A service to identify candidate protein-peptide interaction sites (online)
  • PepCrawler: A fast RRT-based algorithm for high-resolution refinement and binding-affinity estimation of peptide inhibitors (online)
  • CABS-dock: server for flexible protein-peptide docking (online)
  • CABS-dock standalone: a toolbox for flexible protein-peptide docking (standalone)
  • PEPOP: mapping of discontinuous epitopes (you may need to contact the authors to get a password)
  • PepSite: prediction of peptide-binding sites from protein surfaces (online)
  • Pepsite2: prediction of peptide-binding sites from protein surfaces (online)
  • GalaxyPepDock: Protein-peptide docking based on interaction similarity (online)
  • BioPepDB repository of bioactive peptides (online)
  • PhyreStorm (find related structure in the PDB) online
  • CoinFold (protein folding using sequence as input) online
  • PEP-FOLD3 (peptide and complexes) online
  • Peptiderive (Derive peptide inhibitors from PPi) online
  • pepMMsMIMIC (peptide to small molecule) online
  • PEPstrMOD: server predicts the tertiary structure of small peptides with sequence length varying between 7 to 25 residues (online)
  • HADDOCPBSA: HADDOCK standalone
  • PLOP (cyclic peptides) standalone
  • PinaColada: Peptide-Inhibitor Ant Colony Ad-hoc Design Algorithm (online)
  • PRODIGY (protein affinity)
  • Smiles2Monomers: a software to infer monomeric structure of polymers from their atomic structure (online standalone)
  • TAGSFREE: Encoding System for Combinatorial Peptide Libraries (standalone)
  • CPPsite (database):cell penetrating peptides online
  • JPred: A Protein Secondary Structure Prediction Server (online)
  • PSIPred: Protein Sequence Analysis Workbench (online)
  • PEP2D: Peptide Secondary Structure Prediction server (online)
  • PEPlife (database of half life) online
  • Rosetta: computational modeling and analysis of protein structures (online)
  • QUARK: ab initio protein structure prediction and protein peptide folding (online)
  • MUSTER: protein threading algorithm to identify the template structures from the PDB library (online)
  • SEGMER: segmental threading algorithm designed to recoginzing substructure motifs from the Protein Data Bank (PDB) library (online)
  • LOMETS: web service for protein structure prediction (online)
  • Cluspro: protein-protein docking and others inlcuding Template-Based Modeling (online)
  • Anti-inflammatory proteins/peptides (antiinflam) online
  • ACCLUSTER for Peptide Binding Site Prediction, online
  • NNAlign (identification linear motifs, amino acid or nucleotide, and align) online
  • GibbsCluster: unsupervised clustering and alignment of peptide sequences, online
  • ClusPro PeptiDock online
  • pepATTRACT (peptide-protein docking) online
  • LoopFinder (investigates loop-mediated PPI) online
  • CPPred-RF (predictor cell-penetrating peptides) online
  • Protein-Sol (predict protein solubility from sequence) online
  • Solubis (reduce protein aggregation through mutation, check for peptides) online
  • AGGRESCAN3D (A3D): prediction of aggregation (proteins) online
  • miPepBase database of Experimentally Verified Peptides Involved in Molecular Mimicry, online
  • Minimotif Miner 4 a million peptide minimotifs and counting, online
  • Protter (interactive protein feature visualization) online
  • DINC 2 (A New Protein-Peptide Docking Webserver) online

3D structure prediction for small chemical compounds

  • Cosmos (online)
  • Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening (pKa...) (standalone)
  • TANGO: TANGO: A high through-put conformation generation and semiempirical method-based optimization tool for ligand molecules (standalone, available from the authors This email address is being protected from spambots. You need JavaScript enabled to view it.)
  • Spores (check structure, protonation, standalone)
  • Chemaxon: (standalone)
  • Balloon: (standalone)
  • Frog2 (standalone and online)
  • Conformator: a novel method for the Generation of Conformer Ensembles (standalone)
  • DataWarrior (standalone)
  • Knodle (standalone automatic perception)
  • Ambitcli (no 3D but Java application for standardization) (standalone)
  • Standardiser: standardize molecules, it requires RDKIt (standalone)
  • Standardize: PubChem chemical structure standardization (online)
  • WebMO: free World Wide Web-based interface to computational chemistry packages (standalone)
  • Q-Chem: comprehensive ab initio quantum chemistry package for accurate predictions of molecular structures, reactivities, and vibrational, electronic and NMR spectra (commercial, standalone)
  • Surflex-Tools (starting with version 4) (standalone)

Structure-based virtual screening

  • MedusaDock 2.0: Efficient and Accurate Protein-Ligand Docking With Constraints (online)
  • disco: Cross Docking Benchmark server (online)
  • Pharmmaker: Pharmacophore modeling model using outputs of druggability simulations. Uses multiple target conformations dependent on the binding poses of probes where they interact during druggability simulations (standalone and online)
  • DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules (after docking) through graph isomorphism (online and standalone linux)
  • FlexAID: structure-based virtual screening (standalone)
  • Taba: A Tool to Analyze the Binding Affinity. Taba is an open source software and makes use of algorithms of supervised machine learning such as least absolute shrinkage and selection operator (Lasso) and elastic net to create a scoring function aimed to be used for a specific protein family (standalone)
  • DeLinker: Deep Generative Models for 3D Compound Design. Takes two fragments or partial structures and designs a molecule incorporating both. The generation process is proteincontext dependent, utilising the relative dis-tance and orientation between the partial structures (standalone)
  • Taba: A Tool to Analyze the Binding Affinity (create machine-learning models targeted to a specific protein system, scoring) (standalone)
  • DockNmine: a Web Portal to Assemble and Analyse Virtual and Experimental Interaction Data, precision medicine (online)
  • Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations (standalone)
  • DENOPTIM: Software for Computational de Novo Design of Organic and Inorganic Molecules (standalone)
  • AutoDock Bias: improving binding mode prediction and virtual screening using known protein–ligand interactions (standalone)
  • LEDOCK: structure-based docking (standalone)
  • CompScore: boosting structure-based virtual screening performance by incorporating docking scoring functions components into consensus scoring (online)
  • DDT: Drug Discovery Tool, a fast and intuitive graphics user interface for Docking (autodock) and Molecular Dynamics analysis (standalone)
  • DLIGAND2: an improved knowledge-based energy function for protein-ligand interactions using the distance-scaled, finite, ideal-gas reference state (rescoring, works better on some targets that are present in the dataset...) (standalone)
  • iRAISE: inverse screening benchmarking data sets
  • PL-PatchSurfer2: A virtual screening program based on local surface matching (standalone)
  • DeepDTA: Deep drug-target binding affinity prediction (standalone)
  • MLSF: Classical scoring functions for docking are unable to exploit large volumes of structural and interaction data. Random Forest (RF)-based Scoring Functions could help. Code and data for reproducing the results of machine-learning vs classical scoring functions on a similarity-based benchmark (standalone)
  • SIEVE-Score :An Improved Method of Structure-based Virtual Screening via Interaction-energy-based Learning (standalone)
  • AutoDock Bias: improving binding mode prediction and virtual screening using known protein-ligand interactions (standalone)
  • PSOVina 2: Chaos-embedded particle swarm optimization approach for protein-ligand docking and virtual screening (standalone)
  • nAPOLI: a graph-based strategy to detect and visualize conserved protein-ligand interactions in large-scale (online)
  • CASF-2016 virtual screening benchmark: The complete CASF-2016 benchmark will be released on the PDBbind-CN web server. Comparative Assessment of Scoring Functions (docking - scoring dataset online)
  • FINDSITEcomb2.0: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules (online)
  • WnS: Systematic exploration of multiple drug binding sites, Wrap 'n' Shake (WnS) (combine AutoDock 4.2.3 and GROMACS)
  • SAMSON: ligand unbinding pathways (standalone)
  • farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods, Fast Amber Rescoring (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
  • PLEC: Protein-Ligand Extended Connectivity fingerprint and its application for binding affinity predictions (standalone)
  • PRODIGY-LIG web server: Large-scale prediction of binding affinity in protein-small ligand complexes (online)
  • Bindscope: structure based protein-ligand binding predictor (use Convolutional Neural Network) (online)
  • SAnDReS Development of a machine-learning, scoring function, to predict Gibbs free energy of binding for protein-ligand complexes (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)
  • KRDS a web server for evaluating drug resistance mutations in kinases by molecular docking (online)
  • POAP :A GNU parallel based multithreaded pipeline of open babel and AutoDock suite for boosted high throughput virtual screening (The ligand preparation module is a unique feature in POAP) (standalone)
  • VSpipe Integrated Resource for Virtual Screening and Hit Selection (AutoDock, standalone)
  • FITTED virtual screening, scoring for metalloenzymes... (FORECASTER Suite, standalone)
  • Parameterize Parameterize small organic molecules to obtain optimized parameters for AMBER and CHARMM force-fields (online)
  • QuickVina-W QVina: fast and can do full surface screening (standalone)
  • Kdeep Predict the binding affinity of a set of ligands docked in a protein using a state-of-the-art neural network-based predictor (deep learning) (online)
  • Surflexstandalone
  • Dockovalent: covalent docking (online)
  • ACFIS :fragment docking (online)
  • AnchorQuery :structure-based design of PPI inhibitors (online)
  • systemsDock: web server for network pharmacology-based prediction and analysis (online)
  • DockThor: Free Web Server for Protein-ligand Docking (online)
  • DrugDiscovery@TACC: Virtual Drug Discovery Portal (online)
  • e-LEA3D: virtual screening with PLANTS, de novo drug design, fragment (online)
  • iDock: structure-based virtual screening powered by fast and flexible ligand docking, tool inspired by AutoDock Vina, with RF score (standalone)
  • MOMA - LigPath: Starting from the model of a protein-ligand complex, MoMA-LigPath computes the ligand exit path from the active site to the protein surface using robotics-inspired algorithms (online)
  • CovalentDock
  • DOCK Blaster: screening with DOCK (online)
  • AutoDock Vina: standalone
  • Smina :Vina-like with scoring tools (standalone)
  • PyRx: virtual screening with Autodock tools (standalone)
  • PLANTS: virtual screening, ant colony optimization (standalone)
  • Panther: A novel tool to predict small molecule binding into proteins (online)
  • DOCK: The Official UCSF DOCK Web-site (standalone for DOCK)
  • 3D-e-Chem-VM: Virtual Machine (VM) encompassing tools, databases & workflows, including new resources developed for ligand binding site comparisons and GPCR research (standalone)
  • Galaxy7TM: Given a GPCR structure and a ligand structure, optimized complex structures are generated by docking and refinement (online)
  • MTiOpenScreen: virtual screening, blind docking with Autodock or Vina (online)
  • SPOT-ligand: Virtual Ligand Screening based on Binding Homology from Protein 3D Structure (online)
  • SPOT-ligand 2 (screening based on Binding Homology) (standalone)
  • iStar iDock: a software-as-a-service platform for general-purpose web applications (standalone and online tools)
  • Rocker : ROC curve visualization (online)
  • Screening Explorer
  • IonCom : Metal Ion-Binding site prediction. Metal ions (Zn2+, Cu2+, Fe2+, Fe3+, Ca2+, Mg2+, Mn2+, Na+, K+) and four acid radical ions (CO32-, NO2-, SO42-, PO43-) (online)
  • MIB: Metal Ion-Binding site prediction and docking server (12 different metal ions) online
  • rDock: Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids (standalone)
  • Dynamic Undocking (DUck): standalone
  • MMsDockBench : DockBench - MMsDockBench is an integrate informatics platform to automatically perform and compare RMDS-based molecular docking performances (benchmark) of different docking/scoring methods (standalone)
  • DockingApp: user-friendly graphical application for carrying out molecular docking and virtual screening tasks, meant to enable non-experienced users to easily perform such activities and browse the docking results via a three-dimensional visualization (with Autodock Vina, standalone)
  • Octopus: virtual screening (VS). It can perform fast and friendly docking simulation. Differently from others VS platforms, Octopus can perform docking simulations of unlimited number of compounds into a set of molecular targets (standalone)
  • CSAR :Resource for Docking and Scoring Development, benchmark datasets
  • D3R :drug design data resource (also for ligand-based, benchmark)
  • Spark-VS (public cloud, large scale)
  • AMMOS2 :tool to refine protein-ligand-water complexes (online)
  • Spresso : Ultrafast Pre-screening Method Based on Compound Decomposition, fragment docking (standalone)
  • WaterDock-2.0 dock water molecules with Vina (PyMol, standalone))
  • WaterDock-2.0 dock water molecules (standalone)
  • Dowser++ (water - hydrate) standalone
  • RF-Score-VS : Random Forest-based scoring function for Virtual Screening (standalone)
  • DSX :DSX (DrugScore) knowledge-based scoring function (online)
  • Convex-PL :knowledge-based potential for protein-ligand interactions (standalone)
  • DEKOIS (datasets for benchmark)
  • DUDE (datasets for benchmark)
  • BoBER (bioisosteric and scaffold hopping replacements, hit2lead, implements an interface to a database of bioisosteric and scaffold hopping replacements) online
  • MolOpt: A web server for drug design using bioisosteric transformation (online)
  • GalaxyDock2 and BP2 Score :hybrid scoring function, protein-ligand docking program that allows flexibility of pre-selected side-chains of ligand using Conformational Space Annealing (binary available, MAc Linux, standalone)

Ligand-based virtual screening & de novo design

  • PubChem3D: search PubChem in 3D (online)
  • Kinase inhibitor models: Machine Learning Models for Accurate Prediction of Kinase Inhibitors with Different Binding Modes. Datasets and models (standalone)
  • KekuleScope: Prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images (standalone)
  • LSC: Large-scale comparison of machine learning methods for drug target prediction on ChEMBL (code and datasets, deeplearning... standalone)
  • HTS_shrink: Fully automatic Distance-Based Boolean Applicability Domain (DBBAD) algorithm for category QSAR (standalone)
  • 3d-qsar.com: a web portal that brings 3-D QSAR to all electronic devices-the Py-CoMFA web application as tool to build models from pre-aligned datasets (standalone and online)
  • open3dqsar: A New Workflow for QSAR Model Development from Small Data Sets: Integration of Data Curation, Exhaustive Double Cross-Validation and A Set of Optimal Model Selection Techniques. Many other tools (standalone)
  • dtclab: A New Workflow for QSAR Model Development from Small Data Sets: Integration of Data Curation, Exhaustive Double Cross-Validation and A Set of Optimal Model Selection Techniques. Many other tools (standalone)
  • GDBMedChem: Medicinal Chemistry Aware Database GDBMedChem (10 million virtual cmpds) (online)
  • BRUSELAS: HPC generic and customizable software architecture for 3D ligand-based virtual screening of large molecular databases (shape similarity searching and pharmacophore screening) (online)
  • smallmoleculesuite: Cheminformatics Tools for Analyzing and Designing Optimized Small-Molecule Collections and Libraries (eg, liganded genome, kinases…) (R shiny online)
  • Faerun Viz of NLP and NLC: MXFP (macromolecule extended atom‐pair fingerprint), a 217‐D fingerprint tailored to analyze large molecules in terms of molecular shape and pharmacophores. Visualize non‐Lipinski PubChem (NLP) and ChEMBL (NLC) interactively using Faerun (online)
  • MXFP SimilaritySearch: perform MXFP nearest neighbor searches IN non‐Lipinski PubChem (NLP) and ChEMBL (NLC) (online)
  • MedPServer: a database for identification of therapeutic targets and novel leads pertaining to natural products (online)
  • FINDSITEcomb2.0: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules (online)
  • PKS Enumerator: cheminformatics tool to generate virtual chemical libraries of macrocycles or macrolides with multiple user-defined constraints (standalone)
  • ChemoTyper: tool that allows for searching and highlighting chemical chemotypes (chemical substructures or subgraphs) in datasets of molecules. Can be used to search for structural alerts (standalone)
  • DPubChem: online QSAR modeling with PubChem assays (online)
  • MolOpt: A web server for drug design using bioisosteric transformation (online)
  • MB-Isoster: A software for bioisosterism simulation (optimize lead compounds in drug research, 2D and 3D) standalone
  • ChemMaps.com: Exploring chemical spaces
  • Sachem a chemical cartridge for high-performance substructure search (standalone)
  • Diversity Genieanalyze cmpds - collection diversity - standalone
  • SwissSimilarity: virtual screening using different approaches, online
  • WDL-RF weighted deep learning and random forest pipeline for bioactivity prediction of GPCR-associated ligand molecules, online
  • LS-align an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening, standalone
  • Automated framework for QSAR (An automated framework for QSAR model building in Knime) standalone
  • Ezqsar: An R Package for Developing QSAR Models Directly From Structures, standalone
  • ChemSAR: an online pipelining platform for molecular SAR modeling - machine learning (online)
  • ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation, online
  • RRegrs: an R package for computer-aided model selection with multiple regression models, standalone
  • QSARINS: build QSAR models - machine learning - standalone
  • camb: Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules, standalone
  • Screenlamp 3D ligand-based virtual screening workflows (requires Omega and Rocs) standalone
  • Cluster (The open source clustering software Cluster 3.0), standalone
  • Molecular Autoencoder (converts discrete representations of molecules to and from a vector representation, deep learning), standalone
  • Recursive Neural Networks (Inner- and Outer Recursive Neural Networks for Chemoinformatics... (deep learning) standalone)
  • Variational autoencoder (VAE) (framework and code for constructing a variational autoencoder (VAE) for use with molecular SMILES... (deep learning) standalone)
  • Mol2vec (an unsupervised machine learning approach to learn vector representations of molecular substructures, deep learning, standalone)
  • Rchemcpp: online structural analoging (structural analogs are compounds having a similar chemical structure to a given query compound) in ChEMBL, Drugbank and the Connectivity Map, online
  • Consent (ligand-based virtual screening with consensus queries) standalone
  • Pharmit pharmacophore mainly pocket-based, online
  • UFSRAT (Ultra-fast Shape Recognition with Atom Types) online
  • Ligvoxel :structural chemical property and binding hotspot mapper based on convolutional neural networks (CNN). Predict 3D ligand physicochemical properties given a protein structure, output can enter Pharmit (pharmacophore search) online
  • pepMMsMIMIC: given a peptide three-dimensional structure, is able to automate a multiconformers three-dimensional similarity search among 17 million of conformers, online
  • SurflexSim: 3D structure comparison, standalone
  • USR-VS (ligand-based virtual screening powered by ultrafast shape recognition), online
  • MLViS (machine learning)
  • Consensus Diversity Plots: This tool will help you to compare and clasify data sets using diversity metrics (i.e. scaffold counts, fingerprints similarity, molecular properties), describe how diverse each data set is and determine which one is the most diverse (online)
  • Activity Landscape Plotter: SAR, activity cliff, hit2lead, online
  • BoBER: bioisosteric and scaffold hopping replacements, hit2lead, online
  • PUMA: Platform for Unified Molecular Analysis online
  • ChemGPS-NP Web: A tool tuned for navigation in biologically relevant chemical space (online)
  • ChemMine: service for analyzing and clustering small molecules by structural similarities, physicochemical properties or custom data types (online)
  • PharmMapper: reversed pharmacophore matching (online)
  • ZINCPharmer: free pharmacophore search software for screening the purchasable subset of the ZINC database. ZINCPharmer can import LigandScout and MOE pharmacophore definitions, as well as identify pharmacophore features directly from structure (online)
  • Pharmer: Efficient and Exact Pharmacophore Search (standalone)
  • PharmaGist: a webserver for ligand-based pharmacophore detection online
  • SMARTSviewer: Visualize Chemical Patterns (online)
  • AURAmol: (molecule shape search) online
  • LiSiCA PyMOL plugin: Ligand-based virtual screening interface between PyMOL and LiSiCA - standalone
  • ChemMapper: a versatile web server for exploring pharmacology and chemical structure association based on molecular 3D similarity method (online but maybe not running?)
  • PhAST: pharmacophore alignment search tool (online)
  • VIDEAN: Visual Analytics in Cheminformatics: User-Supervised Descriptor Selection for QSAR Methods (online)
  • DWFS: a wrapper feature selection tool based on a parallel genetic algorithm (online)
  • wwLig-CSRre: a 3D ligand-based server for hit identification and optimization (online)
  • iDrug: a web-accessible and interactive drug discovery and design platform (online, still running?)
  • ChemmineR: Cheminformatics Toolkit for R (standalone)
  • Dimorphite-DL: an open-source program for enumerating the ionization (protonation) states of drug-like small molecules (standalone, requires RDKIT)
  • OpenBabel: file format and more, standalone
  • Unicon: command-line tool to cope with common cheminformatics tasks (convert file format, file conversion between standard formats SDF, MOL2, SMILES, PDB, and PDBx/mmCIF via the generation of 2D structure coordinates and 3D structures to the enumeration of tautomeric forms, protonation states, and conformer ensembles, standalone)
  • webDrugCS: Interactive 3D-Visualization of DrugBank chemical space in the web browser (online)
  • Xfp-Browsers: for pharmacophore similarity search online
  • 3D-APfp-Browsers: for shape similarity search online
  • MQN Mapplets: similarity search standalone
  • Multi Fingerprint Browsers: online
  • cApp (analyze collections, clustering...) standalone
  • molBLOCKS (fragments, clusters...), standalone
  • MayaChemTools: similarity search, descriptors, etc, standalone
  • KNIME (eg., HitSEE...), workflow, etc, standalone
  • FAF-Drugs4 and FAF-QED prepare compound collections, filtering etc online
  • Ambitcli no 3D but Java application for standardization, standalone
  • Ambit-Tautomer (Ambit2), standalone
  • Molecule Validation and Standardization (MolVS) standalone
  • chEMBL standardiser: standalone
  • PubChem Standardization Service: online
  • CORINA Symphony Descriptors, calculates a set of molecular descriptors (in total 200) by processing a file of chemical structures in SDF or SMILES format (online)
  • PaDEL descriptors (standalone)
  • Mordred: a molecular descriptor calculator (standalone)
  • CVAE: Molecular generative model based on conditional variational autoencoder for de novo molecular design (standalone)
  • PyDPI : Freely Available Python Package for Chemoinformatics, Bioinformatics, and Chemogenomics Studies (descriptors proteins, ligands, computation of fingerprints...) standalone
  • Mold2 (descriptors from a two-dimensional chemical structure) standalone
  • OpenGrowth (de novo ligand design) standalone
  • ALATIS: Atom Label Assignment Tool using InChI String, duplicate, online
  • HybridSim-VS: combines 2D fingerprint and 3D shape-based similarity, online (still running?)
  • LigQ: A Webserver to Select and Prepare Ligands for Virtual Screening (online)

ADME-Tox

  • hERG: hERG prediction model (input smiles), online
  • hERG data and models 2018: The Catch-22 of Predicting hERG Blockade Using Publicly Accessible Bioactivity Data (python, standalone)
  • NaPLeS: a natural products likeness scorer (online and database)
  • toxFlow: A Web-Based Application for Read-Across Toxicity Prediction Using Omics and Physicochemical Data (online)
  • InAADR: An Adverse Drug Reactions database for Drugs and Proteins (online)
  • VARIDT: variability of drug transporter database (online)
  • MolOpt: A web server for drug design using bioisosteric transformation (online)
  • CardPred: Computational determination (neural network) of hERG-related cardiotoxicity of drug candidates (dataset composed of 2130 compounds) (online)
  • CuDDI: a CUDA-Based Application for Extracting Drug-Drug Interaction Related Substance Terms from PubMed Literature (standalone)
  • FAF-Drugs4: PAINS, Veber, rule of 5, ppiHit profiler, 3/75, structural alerts, oral, phospholipidosis... traffic light... (it prepares cmpd collections and helps select molecules for optimization, remove duplicate, draw a compound and analysis...and FAF-QED) (online, input SDF or smiles)
  • ChemAGG: Structural Analysis and Identification of Colloidal Aggregators in Drug Discovery (and 12,119 aggregator structures in smiles, supplement file of the article) (online)
  • Decagon: Modeling polypharmacy side effects (drug–drug interactions) with graph convolutional networks (standalone)
  • LIVERTOX: up-to-date, accurate, and easily accessed information on the diagnosis, cause, frequency, patterns, and management of liver injury attributable to prescription and nonprescription medications (online)
  • PerMM: A Web Tool and Database for Analysis of Passive Membrane Permeability and Translocation Pathways of Bioactive Molecules (online)
  • AOP-Wiki: adverse outcome pathway (online)
  • AOP-KB: Adverse Outcome Pathway Knowledge Base (OECD) (online and standalone)
  • AOPXplorer: Visualize Adverse Outcome Pathway Networks in Cytoscape (standalone)
  • Skin Doctor: Prediction of skin sensitization potential (online)
  • GLORY: Generator of the Structures of Likely Cytochrome P450 Metabolites Based on Predicted Sites of Metabolism (online)
  • PTP: Predicting Off-Target Binding Profiles With Confidence Using Conformal Prediction (online) (safety pharmacological profiling server about 30 targets)
  • eToxPred: a machine learning-based approach to estimate the toxicity of drug candidates (standalone)
  • Vienna LiverTox Workspace: Transporters expressed in the liver play a major role in drug pharmacokinetics and are key for maintaining bile flow. Inhibition of these transporters may lead to liver toxicity and drug-drug interactions. Various machine learning models can be used...Transporters are P-glycoprotein (Pgp), BCRP, OATP, MRP, ... and models include DILI, cholestasis, hyperbilirubinemia (online)
  • Abstract Sifter: a comprehensive front-end system to PubMed (standalone, Microsoft Excel Windows)
  • NP-Scout: Machine Learning Approach for the Quantification and Visualization of the Natural Product-Likeness of Small Molecules (online)
  • GUT-DOCK-A: Potential off-target effects of beta-blockers on gut hormone receptors: In silico study including GUT-DOCK-A web service for small-molecule docking (online)
  • Hit Dexter 2.0: Machine-Learning Models for the Prediction of Frequent Hitters (online)
  • FungiPAD: A free web tool for compound property evaluation and fungicide-likeness analysis (online)
  • InsectiPAD: A Web Tool Dedicated to Exploring Physicochemical Properties and Evaluating Insecticide-Likeness of Small Molecules (online)
  • SMARTCyp 3.0: Enhanced cytochrome P450 site-of-metabolism prediction server (online)
  • oral toxicity: Acute oral systemic toxicity dataset (standalone for Matlab)
  • hERGdb: integrated database for hERG blocking small molecules and predictions (on the way) (online)
  • VEGA: provides tens of QSAR models to predict tox, ecotox, environ, and phys-chem properties of chemical substances (standalone)
  • SARpy: automatic extraction of Structural Alerts (mainly Windows but also Unix standalone)
  • Pred-hERG: machine learning to predict hERG (online)
  • QSAR tools: a list with some ADME-tox software packages and datasets for toxicity prediction
  • Tox21: Tox21's 10,000-compound library (Tox21 10K 2014) to build models and look for structure-activity relationships (online datasets)
  • ADMETlab: Systematic ADMET evaluation based on a comprehensively collected ADMET database (numerous models, Caco-2, Pgp, Skin, Ames, DILI....) online, input smiles or SDF
  • CTD: The Comparative Toxicogenomics Database is a premier public resource for literature-based, manually curated associations between chemicals, gene products, phenotypes, diseases, and environmental exposures (online)
  • Tdm: a R package for therapeutic drug monitoring, can be used to estimate individual pharmacokinetic / pharmacodynamic (PK/PD) parameters with one or more drug serum/plasma observation obtained from a single subject or multiple subjects using JAGS interfaced through rjags (standalone)
  • HepatoPred-EL: prediction of chemical Hepatotoxicity using ensemble learning methods (online, input smiles)
  • CDPBC :A Software for Estimation of Concentration Dependent Plasma Binding Capacity of Small Molecule via docking (standalone)
  • ToxPi: ToxPi Graphical User Interface 2.0: dynamic exploration, visualization, and sharing of integrated data models (standalone)
  • ChemoTyper: tool that allows for searching and highlighting chemical chemotypes (chemical substructures or subgraphs) in datasets of molecules. Can be used to search for structural alerts (standalone)
  • eMolTox (174 predictions - off targets): In silico Drug Safety Analysis System (online, input smiles)
  • DDI predictor :a tool to optimize drug prescription (A tool to optimize drug prescription - CYP) (online)
  • MetStabOn :metabolic stability predictions (predict t1/2 of compounds) (online, input SDF)
  • CLC-Pred: in silico prediction of human cell line cytotoxicity (online, input smiles and mol files)
  • OPERA: OPEn (q)saR App (models for predicting physicochemical preperties and environmental fate endpoints) (standalone)
  • cBinderDB: a covalent binding agent database (online)
  • CompTox Chemistry Dashboard :a community data resource for environmental chemistry (online)
  • Hit Dexter :Machine-learning Model for the Prediction of Frequent Hitters (online, input smiles)
  • vNN: Web Server for ADMET Predictions (variable nearest neighbor, cytotoxicity, mutagenicity, cardiotoxicity, drug-drug interactions, microsomal stability, and drug-induced liver injury), online, requires login
  • ADVERPred :prediction of adverse effects of drugs (use black box warning...) (such as Arrhythmia, Cardiac failure, Hepatotoxicity, Myocardial infarction, Nephrotoxicity and Myocardial infarction) online, input smiles or other files
  • ADReCS-Target : The Adverse Drug Reaction Classification System-Target Profile provides comprehensive information about ADRs caused by drug interaction with protein, gene and genetic variation (online, running?)
  • NPASS: natural product activity and species source database (online)
  • MouseTox :cytotoxicity assessment for small molecules (online, input smiles)
  • ROSC-Pred :rodent organ-specific carcinogenicity prediction, based on PASS (online, input smiles or mol)
  • VirtualToxLab :3D ADMET, hERG, CYP...
  • LimTox : text mining adverse event and toxicity associations of compounds, drugs and genes (online)
  • FAME2: Effective Machine Learning Model of Cytochrome P450 Regioselectivity (standalone available from authors)
  • FAME 3: Predicting the Sites of Metabolism in Synthetic Compounds and Natural Products for Phase 1 and Phase 2 Metabolic Enzymes (online and standalone)
  • Pred-Skin :chemically-induced skin sensitization (online, input smiles)
  • IDAAPM: Integrated database for ADMET and adverse effect predictive Modeling (online)
  • FDALabel: Online Label Repository
  • DrugBank: approved and experimental drugs (online)
  • DrugCentral: approved drugs (online)
  • NCATS Inxight: incorporates and unifies a wealth of data, including manually curated data supplied by the FDA and private companies, and provides marketing and regulatory status, rigorous drug ingredient definitions, biological activity, clinical use... (online)
  • AquaSolWeb (UG-RNN, predict aqueous solubility, deep learning) (online input smiles)
  • XenoSite (metabolism P450, UGT) (online, input smiles)
  • MLViS (can classify molecules as drug-like and nondrug-like based on various machine learning methods) (online)
  • ADME SARfari : Predict likely ADME targets for an input molecule (online but does not seem to work?)
  • DruLiTo : Predict drug-likeness of a compound (RO5, MDDR rules, Veber rules, Ghose, BBB rule, CMC-50 rule, QED) (standalone)
  • ProTox-II : a webserver for the prediction of toxicity of chemicals (online)
  • Alkemio : Association of chemicals with biomedical topics by text and data mining (online)
  • PAINS-Remover: PAINS compounds
  • ACD/I-Lab : ADME, physchem (online, requires login)
  • SwissADME : Compute physicochemical descriptors as well as predict pharmacokinetics properties and druglike nature of one or multiple small molecules (BBB, Cyp, Pgp...) (online, input smiles)
  • Solubility via OCHEM (also structural alerts, plasma binding, BBB...CYP, AMES..) optimization of compounds via cmpd matched pairs, MolOptimiser) (online)
  • Eli Lilly Open Innovation (medchem: structural alerts and drug-likeness) online via FAF-Drugs4 or Tripod
  • Eli Lilly medchem rules implemented at Tripod (online input smiles)
  • Lilly-MedChem-Rules standalone distribution
    Thanks to Greg Durst for pointing to the Lilly-MedChem-Rules stand-alone command line utility titled 'tsubstructure' which lets you search very large SMILES files for specific SMARTS queries
  • Aggregator Advisor: online, input smiles
  • Pains and aggretators via Zinc: online, input smiles
  • ToxCreate (Acute dermal toxicity, Acute oral toxicity, Blood-brain barrier penetration, Carcinogenicity, DNA-binding, Eye irritation/corrosion, Mutagenicity) (online, input smiles)
  • The HExpoChem server contains information on diverse sources of chemicals with the aim to explore human health risk from chemical exposure (online, input smiles)
  • QED: quantitative estimation of drug-likeness (online input SDF)
  • DrugMint is a web server developed for predicting drug-likelihood of a compound (online)
  • Mcule property calculator (online, input smiles)
  • RS-WebPredictor: Predict cytochrome P450-mediated sites of metabolism on drug-like molecules (online, input SDF)
  • OSIRIS Property Explorer (standalone, the tool is also part of DataWarrior)
  • Toxtree online
  • DrugLogit Calculators (druglikeness) (online)
  • SmartsFilter (many structural alerts and PAINS) (online)
  • PharmGKB is a comprehensive resource that curates knowledge about the impact of genetic variation on drug response for clinicians and researchers (online)
  • Interaction (site 1, 2 and 3) with Serum albumin : predict sites 1, 2, 3 (online)
  • CypRules: A rule-based P450 inhibition prediction server (2015, online and the standalone is also available)
  • pkCSM: predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures (online, input smiles)
  • PASS: predicts over 4000 kinds of biological activity, including pharmacological effects, mechanisms of action, toxic and adverse effects, interaction with metabolic enzymes and transporters, influence on gene expression (online)
  • admetSAR 2.0: web-service for prediction and optimization of chemical ADMET properties (online)
  • ADMETopt: a webserver that can be used to optimize compounds using scaffold hopping while monitoring some ADMETox properties including a drug-likeness score (QED) and synthetic accessibility (multiparameter-like) (online)
  • Construction and analysis of a human hepatotoxicity database suitable for QSAR modeling using post-market safety data (model to do, see the reference)
  • Transformer: Metabolism of Xenobiotics Database (online)
  • DailyMed provides high quality information about marketed drugs (online)
  • The BioZyne P-gp server uses a Support Vector Machine classifier
    to predict whether a compound is likely to be a substrate of the P-gp drug efflux pump (online, input smiles)
  • BADAPPLE (related to PAINS, search for promiscuous cmpds) (online, input mol)
  • Molinspiration (physchem, bioactivity predictions on kinases, ion channels, enzyme, nuclear receptors, GPCR, proteases) (online, input smiles)
  • SOMP is a web-service for in silico prediction of site of metabolism (SOM) (CYPs) (online, input smiles)
  • SOM prediction (CYPs) (online)
  • CredibleMeds.org QTdrugs (torsadogenic risk) lists (hERG related, online)
  • Statistical data mining of Adverse Event Reporting System (AERS Spider)
    is a public online analytical tool which is based on publicly available AERS data
  • CompTox Dashboard (EPA, online))
  • Some web servers for the prediction of drug–drug interactions (DDI)
  • SuperCYP A collection of CYP enzymes and a tool to analyze cytochrome P450-mediated DDI, the new version is Transformer, see above the URL
  • BCRP Human breast cancer resistance protein (BCRP) is an ATP-binding cassette (ABC) efflux transporter that confers multidrug resistance in cancers,
    and also plays an important role in the absorption, distribution and elimination of drugs. The server allows the users to predict whether a query compound is a wild-type BCRP substrate (online)
  • INDI Informatics-based prediction on CYP-related PK DDI (Inferring novel drug-drug interactions) (online)
  • DDI-CPI Web tool for DDI (drug-drug interactions) prediction using molecular docking (online needs login)
  • Human Intestinal Transporter Database QSAR models to predict drug interactions mediated by transporters - Accessed through Chembench (online needs login)
  • admetSAR1 A large number of ADME/Tox QSAR models (online, see also above for version 2)
  • OCHEM Many ADME/Tox QSAR models (online)
  • Virtual Pharmacist: a web tool that interprets personal genome for the impact of genetic variation on drug response (online requires login
  • UCSF-FDA TransPortal: FDA Transporter Database (online)
  • Metabolic stability-Half life (CACTUS (online))
  • Gusar antitargets, rat toxicity...(prediction of antitargets interaction profiles), online
  • Connection Map for Compounds (CMC) online
  • e-Drug3D-PK: Structure-Pharmacokinetic Parameters Data Set (online)
  • Dark chemical matter datasets (supplement data, interesting for PAINS...etc)
  • CIPA (hERG cmpds database) (online)
  • Drug-Induced Liver Injury Network (Dilin) (data online)
  • Endocrine Disruptome: predicts endocrine action of molecules against 16 structures, belonging to 12 nuclear receptors (online, input smiles)
  • Metatox (predict metabolites and toxicity of metabolites, way2drug) (online)
  • hERGscreen (3D pharmacophore models, natural products), some data online
  • CarcinoPred-EL (carcinogenicity of chemicals) (online input smiles)
  • Drug Interaction Database (commercial)
  • TOXNET Databases (Hazardous Substances...) online
  • The eTOX project (develops a drug safety database) (online)
  • PharmaADME.org (ADME gene list, online)
  • Drug Interaction Database - DIDB (metabolism & transport, online)
  • Open TG-GATEs (toxicogenomics, online)
  • Pharmacogenetics Database (e-PKGene)
  • JAPIC (side effects, online)
  • Look at your compounds with standalone tools:
    DataWarrior, ...ICM chemistry,.. Many tools are also included in the Chemaxon packages

Compound collections, medicinal drugs & pharmacology/protein databases

  • IUPHAR: expert-driven guide to pharmacological targets and the substances that act on them (online)
  • HybridMolDB: A Manually Curated Database Dedicated to Hybrid Molecules for Chemical Biology and Drug Discovery (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)
  • Kinome Render: look at kinase family (standalone)
  • PathBank: a comprehensive pathway database for model organisms. new, comprehensive, visually rich pathway database containing more than 110 000 machine-readable pathways found in 10 model organisms. Each small molecule is hyperlinked to the rich data contained in public chemical databases such as HMDB or DrugBank and each protein or enzyme complex is hyperlinked to UniProt (online)
  • MeLAD: an integrated resource for metalloenzyme-ligand associations (database online)
  • Kinase Atlas: contains solvent mapping results for all kinases in the Protein Data Bank. You can search this database by PDB ID or by UniProt accession number (online)
  • CCLE: Cancer Cell Line Encyclopedia (online)
  • GUILDify v2.0: A Tool to Identify Molecular Networks Underlying Human Diseases, Their Comorbidities and Their Druggable Targets (online)
  • YaTCM: Yet another Traditional Chinese Medicine Database for Drug Discovery (online)
  • RESPIRE: Repository of Enriched Structures of Proteins Involved in the Red Blood Cell Environment (online database)
  • Kinmap: interactive navigation through human kinome data (online)
  • PKIDB: a Curated, Annotated and Updated Database of Protein Kinase Inhibitors in Clinical Trials (online)
  • BIOFACQUIM: novel compounds databse with natural products isolated and charcterized in Mexico (online)
  • CH/PMUNK: A Virtual Synthesizable Small-Molecule Library for Medicinal Chemistry, Exploitable for Protein-Protein Interaction Modulators (online)
  • nAPOLI: a graph-based strategy to detect and visualize conserved protein-ligand interactions in large-scale (online)
  • The Pathogen Box: contains ~400 diverse, drug-like molecules active against neglected diseases of interest and is available free of charge (ADME-Tox annotated) (online dataset)
  • ALMANAC: The National Cancer Institute ALMANAC: A Comprehensive Screening Resource for the Detection of Anticancer Drug Pairs with Enhanced Therapeutic Activity (online)
  • GDB-17: 166.4 billion virtual molecules (online)
  • MedPServer: a database for identification of therapeutic targets and novel leads pertaining to natural products (online)
  • ClinicalTrials.gov: registry of clinical trials (online)
  • BitterDB: taste ligands and receptors database (online)
  • V1M: Virtual 1 million macrolide - macrocycles scaffolds (online as suppl file with smiles
  • WebCSD: the on-line portal to the Cambridge Structural Database (CSD), small molecule experimental 3D structures (online)
  • NR-DBIND: Nuclear Receptors Database Including Negative Data
  • Pfam: The Pfam protein families database (online)
  • KinaMetrix: a web resource to investigate kinase conformations and inhibitor space (online)
  • ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms’ proteomes (online)
  • COD: Crystallography Open Database (online)
  • IUPAC: IUPAC Compendium of Chemical Terminology - the Gold Book
  • NextProt: Exploring the universe of human proteins
  • SMMDB: a web-accessible database for small molecule modulators and their targets involved in neurological diseases
  • MobiDB :a database of protein disorder and mobility annotations
  • DrugAge :Database of ageing-related drugs
  • ChemMaps.com: Exploring chemical spaces
  • CircadiOmics: circadian omic web portal
  • DT-Web: DT-Web: a web-based application for drug-target interaction and drug combination prediction through domain-tuned network-based inference (periodically synchronized with DrugBank and PathwayCommons) (online)
  • Therapeutic Target Database (TTD): target and compound data (online)
  • ApoCanD: Database of Human Apoptotic Proteins in the context of cancer
  • Supertarget: an extensive web resource for analyzing 332828 drug-target interactions (displays also pathways, load KEGG, map drugs onto these pathways) (online)
  • GenBank: NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (online)
  • PROSITE: Database of protein domains, families and functional sites (online)
  • SCOP2: Structural Classification of Proteins 2 (online)
  • EMBL-EBI services: many tools for proteins, sequences... (online)
  • OMIM: Online Mendelian Inheritance in Man (online)
  • NPC: the NCGC Pharmaceutical Collection is a comprehensive, publically-accessible collection of approved and investigational drugs
  • KampoDB: database of predicted targets and functional annotations of natural medicines (online)
  • SynPharm: open web resource mainly designed to help synthetic biologists to engineer pharmacological regulation into their proteins (online)
  • NPASS: natural product activity and species source database (online)
  • Super Natural II: a database of natural products (online)
  • HIT: Herbal Ingredients' Targets Database (online)
  • VIETHERB: A Database for Vietnamese Herbal Species - Natural products (online)
  • TCM Database@Taiwan: the world's largest traditional Chinese medicine database for drug screening in silico (online)
  • iSMART: an integrated cloud computing web server for traditional Chinese medicine for online virtual screening, de novo evolution and drug design (online)
  • Nubbe: a natural products database from the biodiversity of Brazil (online)
  • ETM-DB: integrated Ethiopian traditional herbal medicine and phytochemicals database (online)
  • COCONUT: Compound Combination-Oriented Natural Product Database with Unified Terminology (COCONUT) contains traditional medicine, combination drug, functional food, and up-to-date molecular drug/target information from heterogeneous sources, providing valuable resources for polypharmacology studies (online)
  • SANCDB: a South African natural compound database (online)
  • NPACT: naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database (online)
  • The Reactome Pathway Knowledgebase: provides molecular details of signal transduction, transport, DNA replication, metabolism, and other cellular processes as an ordered network of molecular transformations
  • DTC: Drug Target Commons (DTC) is a crowd-sourcing platform to improve the consensus and use of drug-target interactions
  • cBinderDB :a covalent binding agent database
  • Drugs-in-3D: Drug and Drug Target Mapping at the PDB
  • 2P2I: Protein-Protein Complexes and their Inhibitors (2P2I database) (online)
  • TIMBAL: Protein-Protein interaction inhibitors (online)
  • iPPI-DB: Protein-Protein interaction inhibitors (online)
  • MOSAIC :a chemical-genetic interaction data repository and web resource for exploring chemical modes of action
  • ProteomicsDB :Human proteins, peptides, inhibitors and analytics
  • FooDB :large resource on food constituents, chemistry and biology
  • AdditiveChem: A comprehensive bioinformatics knowledge-base for food additive chemicals (about 9000) (online)
  • NutriChem 2.0 :exploring the effect of plant-based foods on human health and drug efficacy (natural product)
  • ChemAgora Portal :Searching Online Chemical Data Repositories
  • jMorp :Japanese Multi Omics Reference Panel (database containing metabolome and proteome data for plasma obtained from >5000 healthy volunteers)
  • THPdb :Database of FDA-approved peptide and protein therapeutics
  • DrugPort :Approved drugs in complex with targets (X-ray structures)
  • dbPTM :Protein post-translational modifications (PTMs) database
  • CATH-Gene3D: Gene3D uses the information in CATH to predict the locations of structural domains on millions of protein sequences available in public databases (Protein domain visualisation in gene trees, Domain architecture pages, multiple sequence alignments mapped in 3D, etc) (online)
  • CATH: classification of protein structures downloaded from the Protein Data Bank (online)
  • WikiPathways :a multifaceted pathway database bridging metabolomics to other omics research (can be seen in Cytoscape) (online)
  • PathVisio: free open-source biological pathway analysis software that allows you to draw, edit and analyze biological pathways (standalone)
  • Pathway Commons: Access and discover data integrated from public pathway and interactions databases (online)
  • Target-Pathogen :a structural bioinformatic approach to prioritize drug targets in pathogens
  • FlavorDB :repository of flavor molecules, their natural sources, physicochemical properties, and sensory responses (about 25,595 flavor molecules)
  • PharmacoDB :Mine multiple cancer pharmacogenomic datasets (to find where a drug or cell line of interest has been profiled, and to view and compare the dose-response data for a specific cell line - drug pair)
  • DISNOR : 3700 disease-pathways, mutations, protein-disease association data..etc
  • HPP :Human Proteome Project (HPP and HUPO)
  • Protein Data Bank Japan (PDBj) (many tools including Molmil, ProMode-Elastic server, Omokage search for molecular shape similarity)
  • Protein Data Bank Europe (PDBe) (many tools)
  • Drug To PDB IDs Mappings: database (online)
  • Protein Data Bank (PDB: many tools and search utilities)
  • ValTrendsDB: bringing Protein Data Bank validation information closer to the user (online)
  • PDB-Dev (a Prototype System for Depositing Integrative/Hybrid Structural Models)
  • UniProt (many tools including genes' ID converter, SNPs, ...)
  • Ensembl (research on vertebrate genomes, SNPs...)
  • MalaCards (human diseases)
  • InterPro (classify protein sequences into families and domains)
  • CDD/SPARCLE (functional classification of proteins, domains)
  • DrugBank: medicinal drugs, experimental drugs...
  • DrugCentral: medicinal drugs
  • DGIdb 3.0 a redesign and expansion of the drug–gene interaction database
  • WITHDRAWN: withdrawn and discontinued drugs
  • ECOdrug a database connecting drugs and conservation of their targets across species
  • SuperDRUG2: a one stop resource for approved/marketed drugs
  • e-Drug3d: offers a facility to explore FDA approved drugs and active metabolites
  • Chembl: annotated compounds, medicinal drugs...
  • CIIPro: a new read-across portal to fill data gaps using public large-scale chemical and biological data (automatically extract in vitro biological data from public resources (i.e. PubChem) for user-supplied compounds) (standalone)
  • PubChem: molecules tested via HTS and more
  • Fetch PubChem compounds
  • Fetch PubChem compounds with Ligdig
  • Chebi: Chemical Entities of Biological Interest
  • KEGG ligand: contains our knowledge on the universe of chemical substances and reactions that are relevant to life
  • PDBeChem: Chemical Components in the PDB
  • HEDD the human epigenetic drug database
  • NPC Pharmaceutical Collection
  • Zinc: a free database of commercially-available compounds
  • Molport: commercially-available compounds
  • eMolecules: commercially-available compounds
  • ChemSpider: commercially-available compounds
  • BioLiP: a semi-manually curated database for high-quality, biologically relevant ligand-protein binding interactions
  • TTD: Therapeutic Target Database
  • SWEETLEAD: An in silico database of approved drugs, regulated chemicals, and herbal isolates
  • DCDB: drug combination database
  • SuperTarget: an extensive web resource for analyzing 332828 drug-target interactions
  • Matador: Manually Annotated Targets and Drugs Online Resource
  • PLIC
  • PoSSuM(pocket comparison online)
  • ProBis: pocket comparison online
  • sc-PDB: An Annotated Database of Druggable Binding Sites from the Protein DataBank
  • PDB: protein databank
  • PDBe: protein databank europe
  • Credo: A Structural Interactomics Database For Drug Discovery
  • PDBbind: comprehensive collection of the experimentally measured binding affinity data for all types of biomolecular complexes deposited in the Protein Data Bank (PDB)
  • PLI: PROTEIN-LIGAND Interaction is a database that describes the interactions that a small molecules (identified by a Het_Id code) perform with target proteins, as observed in PDB complexes
  • FDALabel: drugs Online Label Repository
  • Binding DB
  • Wikipedia chemical structure explorer: online tool to explore chemicals from Wikipedia
  • BioGRID: curated set of data have been updated to include interactions, chemical associations, and post-translational modifications (PTM) from many publications
  • SBKB: Structural Biology Knowledgebase
  • Pharos (druggable genome)
  • OpenTargets platform: Find new targets for drug discovery
  • 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
  • ExCAPE-DB chemogenomics database (online)
  • ExCAPE-DB chemogenomics database (datasets)
  • Chemical Probes: Chemical Probes Portal is designed to change the way scientists find and use small-molecule reagents called chemical probes in biomedical research and drug discovery
  • Consensuspathdb: integrates interaction networks in Homo sapiens including binary and complex protein-protein, genetic, metabolic, signaling, gene regulatory and drug-target interactions, as well as biochemical pathways
  • Pathguide: Pathguide contains information about 702 biological pathway related resources and molecular interaction related resources
  • Cancer Cell Map Initiative (CCMI)
  • DTome: Drug-Target Interactome
  • Genomics, Evidence, Neoplasia, Information, Exchange (GENIE)
  • NPCARE: database of natural products (cancer)
  • LOINC (common language clinical and laboratory)
  • Chemical Identifier Resolver (CIR)
  • Aggregate Analysis of ClincalTrials.gov (AACT)
  • The Small Molecule Pathway Database (SMPDB)
  • Fragment Database FDB-17 (10 million)
  • TargetMine (tools for target prioritization)
  • InfoRNA (ligands for RNA)
  • UniChem (cross-references between chemical structure identifiers from different databases)
  • Minepath.org (interactive pathway analysis)
  • XTalkDB: a database of signaling pathway crosstalk
  • Drugs.com :data about drugs and clinical trials (check also drugs.com for drug-drug interactions, DDI), online
  • SMMRNA: a database of small molecule modulators of RNA
  • DrugKiNET (kinase inhibitors)
  • Nucleic acid ligand database (NALDB)
  • Probes & Drugs portal: a public resource joining together focused libraries of bioactive compounds (probes, drugs, specific inhibitor sets etc.) with commercially available screening libraries. The purpose of the portal is to reflect the current state of bioactive compound space and to enable its exploration from different points of view

Repositioning, repurposing,
polypharmacology, target fishing, drug combination

  • MTiOpenScreen (repositioning): Online structure-based screening of purchasable approved drugs and natural compounds: retrospective examples of drug repositioning on cancer targets (online)
  • ACID: a free tool for drug repurposing using consensus inverse docking strategy (online)
  • Drug-Class: Learning Drug Functions from Chemical Structures with Convolutional Neural Networks and Random Forests (standalone)
  • Centerwatch: Prescription drugs and drugs approved by the FDA by year - Database (online)
  • DIA-DB: prediction of diabetes drugs (ligand-based and inverse screening) (online)
  • DailyMed: provides trustworthy information about marketed drugs in the United States - Database (online)
  • DeepScreening: a deep learning-based screening web server for accelerating drug discovery (online)
  • DRUDIT: Web-Based DRUgs DIscovery Tools to Design Small Molecules as Modulators of Biological Targets, Multi-Target and On/Off-Target tasks (online, need password)
  • LSC: Large-scale comparison of machine learning methods for drug target prediction on ChEMBL (code and datasets, deeplearning... standalone)
  • MuSSel: Multi-fingerprint Similarity Search aLgorithm, tool to find putative protein drug targets of small molecules or to repurpose (reposition) existing bioactive compounds. Target fishing, polypharmacology (online)
  • CancerDrugMap: Extended Multitarget Pharmacology of Anticancer Drugs (online)
  • X2K: Web infers upstream regulatory networks from signatures of differentially expressed genes (standalone)
  • DeepCOP: deep learning-based approach to predict gene regulating effects of small molecules (standalone)
  • deepDR: A network-based deep learning approach to in silico drug repositioning (standalone)
  • DrugZ: DrugZ is an open-source Python software for the analysis of genome-scale drug modifier screens. The software accurately identifies genetic perturbations that enhance or suppress drug activity. Identifying chemogenetic interactions from CRISPR screens with drugZ (standalone)
  • CRDS: Consensus Reverse Docking System for Target Fishing (reverse docking against 5254 target proteins for one given ligand ID from PubChem or ZINC) (online)
  • EK-DRD: A Comprehensive Database for Drug Repositioning Inspired by Experimental Knowledge. EK-DRD contains experimentally validated drug repositioning annotation for 1861 FDA-approved and 102 withdrawn small molecule drugs. Annotation is done at four levels, using 30,944 target assay records, 3999 cell assay records, 585 organism assay records, and 8910 clinical trial records (online)
  • ReactomeFIViz: drug-target visualization in the context of pathways and networks (integrates drug-target interaction information with high quality manually curated pathways and a genome-wide human functional interaction network). Both the pathways and the functional interaction network are provided by Reactome (Reactome Cytoscape app standalone)
  • Bioactivity-explorer: a web application for interactive visualization and exploration of bioactivity data (from ChEMBL, network, disease…) (online and standalone)
  • PPB2: Polypharmacology prediction (online)
  • PROTEINATOR: enables repurposing of leads based on secondary interactions. Direct Drugs are listed and Indirect Drugs (Compounds that bind to the 'first-neighbour' of the primary protein(s)) (online)
  • PatchSearch: a web server for off-target protein identification (input a protein complexed with a ligand and identifies within user-defined or predefined collections of protein structures, those having a binding site compatible with this ligand in terms of geometry and physicochemical properties) (online)
  • Drug ReposER: web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning (pocket comparison, ligand transposition) (online)
  • CSgator: an integrated web platform for compound set analysis, can be used for toxicity and investigate polypharmacology (online)
  • DrugComb: an integrative cancer drug combination data portal (online)
  • MolTarPred: a web tool for comprehensive target prediction with reliability estimation (online)
  • DEEPScreen: Virtual Screening Using Convolutional Neural Networks By Images of Compounds (standalone)
  • TIN-X: target importance and novelty explorer (prediction via text mining) (online)
  • DrugR+: database for drug repurposing, combination therapy, and replacement therapy (online)
  • ReDO_DB: the repurposing drugs in oncology database (online)
  • Target2: Predicting protein targets for drug-like compounds using transcriptomics (LINCS Data) (data set)
  • Drug Targetor: a web interface to investigate the human druggome for over 500 phenotypes
  • PathwayMap: Fast prediction of the interaction between a set of ligands (similarity) and major human biological and signaling pathways using state-of-the-art neural networks (online)
  • DTP: Interactive visual analysis of drug–target interaction networks using Drug Target Profiler, with applications to precision medicine and drug repurposing (online)
  • CONNECTOR: predicts propensity of putative drug-protein interactions based on similarity between the input drug structure, drug profile, and/or protein sequence and the experimental drug-protein interactions that are included in the internal database (online)
  • DIGREM: Drug-Induced Genomic Response models for identification of Effective Multi-drug combinations, an online tool kit that can effectively predict drug synergy (online)
  • HitPickV2: a Web Server to predict targets of chemical compounds (polypharmacology, profiling), input smiles (online)
  • Drug-Target Explorer: DTexplorer, Probing the chemical–biological relationship space (phenotypic screening, polypharmacology, prediction of molecular targets for novel molecules based on structural similarity (online)
  • PharmacoDB: Mine multiple cancer pharmacogenomic datasets (to find where a drug or cell line of interest has been profiled, and to view and compare the dose-response data for a specific cell line - drug pair) (online)
  • SynergyFinder: a web application for analyzing drug combination dose-response matrix data (online)
  • CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets (online)
  • Combenefit: an interactive platform for the analysis and visualization of drug combinations (for windows) standalone
  • DRRS: Computational drug repositioning using low-rank matrix approximation and randomized algorithms (standalone)
  • ChemMapper: a versatile web server for exploring pharmacology and chemical structure association based on molecular 3D similarity method (online, still running?)
  • ChemProt 3: a ressource of annotated and predicted chemical-protein interactions (input can be SMILES, online)
  • Similarity ensemble approach (SEA): the approach relates proteins based on the set-wise chemical similarity among their ligands (online)
  • Open Targets: visualisation of potential drug targets associated with disease (online)
  • DrugDiseaseNet: a novel computational approach for drug repurposing using systems biology (R package) (standalone)
  • eRepo-ORP: contains data generated for the repositioning of DrugBank drugs to Orphanet proteins (online data)
  • RF QSAR: random Forest QSAR models for target identification and fishing (target deconvolution in phenotypic screening, polypharmacology, repositioning), 1121 human targets were built by random forest algorithm using bioactivity data from ChEMBL (input smiles, online)
  • Chemotext: Publicly-Available Web Server for Mining Drug-Target-Disease Relationships in PubMed (polypharmacology, repositioning...) (online)
  • TargetNet: a web service for predicting potential drug-target interaction profiling via multi-target SAR models. When the user submits a molecule, the server will predict the activity of the user’s molecule across 623 human proteins by establishing the high quality QSAR model for each human protein (thus 623 QSAR models), thus generating a DTI profiling that can used as a feature vector for wide applications (online)
  • Probe Miner: Objective Assessment of Chemical Probes. This resource provides evaluation of > 1.8m small molecules against for >2,200 human targets (online, input target name)
  • PhID: Integrated Pharmacology Interactions Database for Drugs, Targets, Diseases, Genes, Side-Effects, and Pathways (visualize, online)
  • DTINet: novel drug–target interactions from a constructed heterogeneous network (standalone)
  • STOPGAP: Systematic Target OPportunity assessment by Genetic Association Predictions (online)
  • ChemViz2: extends the capabilities of Cytoscape into the domain of cheminformatics (Cytoscape App, standalone, help to visualize data)
  • DRAR-CPI: This server has a representative collection of drug molecules and targetable human proteins. When you submit a molecule, the server will suggest candidate off-targets that tend to interact with it, and will also give the positive or negative association scores between your molecule and our library drugs based on their interaction profiles of the CPI. Since our library drugs have annotations of their indications and ADRs, you can thus predict new indications or unknown ADRs based on the association scores of your molecule across our library molecules (need registration, online)
  • AVCpred: Antiviral compound prediction via QSAR (input SDF, online)
  • HitPick: web server that facilitates the analysis of chemical screenings by identifying hits and predicting their molecular targets. The target prediction functionality can also be used in a stand-alone fashion (online and standalone, input smiles)
  • idTarget: A web server for identifying biomolecular targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach (online)
  • SPiDER: self-organizing map–based prediction of drug equivalence relationships (online)
  • Mantra: computational tool for the analysis of the Mode of Action (MoA) of novel drugs and the identification of known and approved candidates for “drug repositioning”. It is based on network theory and non-parametric statistics on gene expression data (online)
  • PASS: predicts over 4000 kinds of biological activity, including pharmacological effects, mechanisms of action, toxic and adverse effects, interaction with metabolic enzymes and transporters, influence on gene expression, etc (online)
  • SwissTargetPrediction: allows to predict the targets of a small molecule. Using a combination of 2D and 3D similarity measures, it compares the query molecule to a library of 280'000 compounds active on more than 2000 targets of 5 different organisms (online)
  • SuperPred: a prediction webserver for ATC code and target predicition of compounds (online)
  • TargetHunter
  • TarFisDock: the Targets Associated with its MOst SImilar Counterparts, by exploring the largest chemogenomical databases (online)
  • DGIdb: Drug gene interactions database. User-friendly browsing, searching, and filtering of information on drug-gene interactions and the druggable genome, mined from over thirty trusted sources (online)
  • FDALabel: Online Label Repository (online)
  • KEGG Drug: comprehensive drug information resource for approved drugs in Japan, USA, and Europe (online)
  • Supertarget: an extensive web resource for analyzing 332828 drug-target interactions (online)
  • MATADOR: Manually Annotated Targets and Drugs Online Resource (online)
  • DrugCentral: search by drug, target name and by pharmacologic action (online)
  • CRIBdb NME: contains useful information regarding NMEs - approved drugs (database online)
  • ChemCom: (Chemical Comparator) is a computer application which facilitates searching and comparing chemical libraries (standalone)
  • DRUGSURV: a resource for repositioning of approved and experimental drugs in oncology based on patient survival information derived from clinical cancer expression datasets (online)
  • DINIES: Drug-target Interaction Network Inference Engine based on Supervised Analysis enables us to predict potential interactions between drug molecules and target proteins, based on drug data and omics-scale protein data (online)
  • BalestraWeb: efficient online evaluation of drug–target interactions (online)
  • LigSearch: Identification of possible ligands from 3D protein structure or sequence (online)
  • systemsDock: web server for network pharmacology-based prediction and analysis, which applies high-precision docking simulation and molecular pathway map to comprehensively characterize the ligand selectivity and to illustrate how a ligand acts on a complex molecular network (online) input 5 small molecules max
  • Ligdig: application for investigating ligand-protein interactions. LigDig can be used to query structural and functional properties, compare binding sites... (online)
  • Drugquest: text mining (online)
  • PLIC: Clusters of similar binding sites in the PDB and analysis of various type of interactions within the clusters (online)
  • PoSSuM: pocket similarity search (online)
  • ProBis: align protein binding site (online)
  • DT-Web: drug target interaction prediction, drug combination (online and standalone, R package)
  • sc-PDB: Annotated Database of Druggable Binding Sites from the Protein DataBank (online)
  • DASPfind: New Efficient Method to Predict Drug-Target Interactions (online)
  • KEGG: Kyoto Encyclopedia of Genes and Genomes (database online)
  • GO: Gene Ontology Consortium (online)
  • UniProt: provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information (online)
  • iGPCR-Drug: Predicting drug-GPCR interaction in cellular networking (input drug code and protein sequence) (online)
  • PDTD: Potential Drug Target Database (online)
  • CancerResource: It is a comprehensive knowledgebase for drug-target relationships related to cancer as well as for supporting information or experimental data (online)
  • Carlsbad: Select either the Targets or Structures tab above to search for targets or structures, respectively (database online)
  • GEO2R: compare two or more groups of Samples in order to identify genes that are differentially expressed across experimental conditions (online)
  • PDID: Protein-Drug Interaction Database in the structural human proteome (similar binding site, docking, inverse docking) (online)
  • iDTP: An integrated structure- and system-based framework to identify new targets of metabolites and known drugs (standalone)
  • iDrug-Target: A package of web-services for predicting drug-target interaction (online)
  • e-LEA3D: docking (online)
  • iDrug: online drug discovery (similarity, pharmacophore..) (online)
  • MANORAA: Mapping Analogous Nuclei Onto Residue And Affinity for identifying protein–ligand fragment interaction, pathways and SNPs (online)
  • DrugTargetInspector: Assistance tool for patient treatment stratification (online)
  • K-Map (KMap, Kinase Map), connecting kinases with therapeutics for drug repurposing and development, input kinase name (online)
  • iATC-mISF (ATC predictor): a multi-label classifier for predicting the classes of anatomical therapeutic chemicals (input smiles, online)
  • iATC-mHyb: hybrid multi-label classier for predicting the classication of anatomical therapeutic chemicals, online
  • Phenolyzer: stands for Phenotype Based Gene Analyzer, a tool focusing on discovering genes based on user-specific disease/phenotype terms (online)
  • Gusar antitargets...developed to create QSAR/QSPR models on the basis of the appropriate training sets represented as SDfile contained data about chemical structures and endpoint in quantitative terms (online, input draw a compound)
  • DRABAL: Novel Method for Mining Large High-throughput Screening Assays using Bayesian Active Learning (standalone)
  • webDrugCS: Interactive 3D-Visualization of DrugBank chemical space in the web browser (online)
  • DTIPRED: Computational Discovery of Putative Leads for Drug Repositioning Through Drug-Target Interaction Prediction (standalone)
  • MeSHDD (text mining) MeSH-based Drug-Drug Similarity and Repositioning (online)
  • PatchSearch (pocket-based) standalone
  • RepoDB (database for drug repositioning) online
  • SIMCOMP/SUBCOMP (target fishing), input mol file, online
  • CSNAP (target fishing), Large-scale Chemical Similarity Networks for Drug Target Profiling of Compounds Identified in Cell-based Chemical Screens (online)
  • Drug Repurposing Hub (online)
  • RepurposeDB (Explore repositioned drug) (online)
  • Off-label and polypharmacy side effect databases (online download) (Offsides)
  • Twosides databases (polypharmacy side effects for pairs of drug, online to download)
  • SIDER (ADR of marketed medicines), contains information on marketed medicines and their recorded adverse drug reactions (online)
  • Phenomizer (clinical diagnostics based on genomics and patient symptomology) online
  • LINCSCLOUD or CLUE.IO (perturbation-driven gene expression dataset, online)
  • PRIME (EMA) unmet medical needs (trials), PRIME is a scheme launched by the European Medicines Agency (EMA) to enhance support for the development of medicines that target an unmet medical need
  • PharmMapper (reversed pharmacophore matching, target fishing) online
  • TargetPred Target Prediction: applications for predicting the function of several targets such as proteins in human diseases or molecular proceses by using protein information (Bio-AIMS) online
  • C-SPADE serves as an interactive and innovative visualization tool for drug screening data. It reterives compounds structural information and clusters them based on their structural similarties, which is later visualized as a dendrogram of compounds augmented with their bioactivity values and other compound annotations (Compound SPecific bioActivity DEndrogram, compounds-phenotype) online
  • PPB Polypharmacology Browser, target prediction (online and standalone)
  • Rephetio: Drug repurposing predictions (online)
  • Hetionet (integrative network of biomedicine) standalone
  • NFFinder: bioinformatics approach that combines experimental gene expression profiles and data from publicly available databases to identify conditions or experiments that induce similar or opposite gene expression patterns (conditions that induce similar or opposite gene expression patterns) (online)
  • CoGe (comparative genomics) online
  • Drug Vs Disease An R and Cytoscape plug-in for comparing Drug and Disease profiles (standalone)
  • Enrichr (datasets of diseases, genes..) online, input BED or list of genes
  • Drugs.com (data about drugs and clinical trials) online
  • DrugSig: drug repositioning with gene expression signatures for drug repositioning (online)
  • Drug voyager: exploring unintended drug action
  • JAPIC (side effects) (online)
  • DrugKiNET (kinase inhibitors) online
  • PDSP Ki database
  • Repurposed Drug Database (online)
  • Drug Repurposing Wiki (online)
  • Drug SIGnatures DataBase (DSigDB: Drug Signatures Database for Gene Set Analysis (online)
  • RE:fine Drugs: drug repurposing opportunities (online)
  • Breakthrough Therapies chart: is a list of all publicly announced breakthrough therapy designations since the program’s inception in 2012 (online)
  • SDTNBI: an integrated network and chemoinformatics tool for systematic prediction of drug-target interactions and drug repositioning (standalone)
  • DTome: Drug-Target Interactome (online)
  • PASS Targets predict interactions online (~1534 human proteins) at Way2Drugs
  • chemogenomicAlg4DTIpred: Open-source chemogenomic data-driven algorithms for predicting drug-target interactions (in R) standalone
  • Selenzyme: a free online enzyme selection tool for metabolic pathway design (online)

"Data manipulation tools - dataviz - machine learning - descriptors - model repository"

  • The Caret package for machine learning (standalone)
  • MOLE db: Molecular Descriptors Data Base is a free on-line database comprised of 1124 molecular descriptors calculated for 234773 molecules (online)
  • ClassyFire: web-based application for automated structural classification of chemical entities (online)
  • Entrezpy: A Python library to dynamically interact with the NCBI Entrez databases (standalone)
  • Raincloud plots: a multi-platform tool for robust data visualization (standalone)
  • FuncTree2: an interactive radial tree for functional hierarchies and omics data visualization (online and standalone, eg, via Docker: https://github.com/yamada-lab/functree-ng)
  • iLearn: an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data (e.g., python tools to compute sequence descriptors with several machine learning approaches) (online and standalone)
  • DOGMA: a web server for proteome and transcriptome quality assessment (online and standalone)
  • VisFeature: a stand-alone program for visualizing and analyzing statistical features of biological sequences (standalone)
  • Physicochemical n-Grams Tool: A tool for protein physicochemical descriptor generation Proteomics Data Analysis Tool (standalone - Windows)
  • Dimorphite-DL: an open-source program for enumerating the ionization (protonation) states of drug-like small molecules (standalone, requires RDKIT)
  • PySpark and RDKit: Moving towards Big Data in Cheminformatics (in the supplement of the article) (standalone)
  • Wordclouds: Wordscloud (online)
  • LSTMs: Visual Analysis for Recurrent Neural Networks (machine learning, standalone and online)
  • Tox21: Tox21's 10,000-compound library (Tox21 10K 2014) to build models and look for structure-activity relationships (online datasets)
  • MER: a shell script and annotation server for minimal named entity recognition and linking (Minimal Entity Recognizer, text mining, standalone)
  • LitSense: making sense of biomedical literature at sentence level (text mining, online)
  • OmicsNet: for Network Integration and 3D Visualization including small molecules (online)
  • FigTree: designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures (standalone)
  • Ambit-SMIRKS: a software module for reaction representation, reaction search and structure transformation (standalone)
  • Chemmodlab: A Cheminformatics Modeling Laboratory for Fitting and Assessing Machine Learning Models (standalone)
  • WebGraphviz: is Graphviz (Graphviz is open source graph visualization software) in the Browser (online)
  • Canva: creative graph design (online)
  • Infogram: creative (animated) graphics (online)
  • Faerun: interactive 3D-Visualization of SureChEMBL in the web browser, also available as a Python package (online)
  • Chemmaps: visualize chemical space (online)
  • ChemSAR: full workflow of building a Structure‑Activity/Property Relationship(SAR/SPR) model (online)
  • ChemDes: An integrated web-based platform for molecular descriptor and fingerprint computation (online)
  • Ezqsar: An R Package for Developing QSAR Models Directly From Structures (computes also descriptors…) (standalone)
  • MLViS: machine learning-based virtual screening tool (online)
  • NAViGaTOR: Network Analysis, Visualization, & Graphing TORonto (standalone)
  • D-Tools: online tools for chemistry and data analysis, PUMA (Platform for Unified Molecular Analysis), Activity Landscape Plotter server (ActLSmaps), Consensus Diversity Plots (CDPS) (online)
  • KNIME: Konstanz Information Miner, is a free and open-source data analytics, reporting and integration platform (standalone), toolkit for drug discovery
  • BlueObelisk: Interoperability in Chemical Informatics (standalone), toolkit for drug discovery
  • CDK: toolkit for drug discovery, descriptors (standalone)
  • OpenBabel: toolkit for drug discovery, file format etc (standalone)
  • ODDT: Open Drug Discovery Toolkit, toolkit for drug discovery (standalone)
  • Joelib: Molecular descriptors (standalone)
  • Afgen: Fragment-based descriptors (standalone)
  • DENOPTIM: Software for Computational de Novo Design of Organic and Inorganic Molecules. Virtual compounds. Also utility to fragment small molecules (standalone)
  • ISIDA - fragmentor: Calculate of Substructural Molecular Fragments and ISIDA Fragments (standalone)
  • Web scraping: How to Scrape an HTML website for Chemical Information (python scripts, standalone)
  • Cytoscape: open source software platform for visualizing complex networks and integrating these with any type of attribute data (standalone)
  • Systematic Review toolbox: tools for systematic reviews, text mining (information)
  • Abstract Sifter: a comprehensive front-end system to PubMed (standalone, Microsoft Excel Windows)
  • The Math : Math Online equation solver (online)
  • Databionic ESOM (Emergent Self-Organizing Maps) (standalone)
  • Venny (Venn diagrams to find data in common) (online and standalone)
  • InteractiVenn: a web-based tool for Venn diagrams (up to 6 datasets - online)
  • ChemDB chemoinformatics portal (chemoinformatics tools & datasets) (online)
  • OCHEM (chemoinformatics tools & datasets, model collections) (online)
  • Shinyheatmap for big data genomics (online)
  • QsarDB repository (online)
  • DeepChem Python library democratizing deep learning for science
  • GUSAR@NIH (chemoinformatics tools & datasets) (online)
  • FUn: A Framework for Interactive Visualizations of Large, High Dimensional Datasets on the Web (online)
  • pdb-tools: command line python scripts to manipulate PDB file (standalone)
  • Lemon: a framework for rapidly mining structural information from the Protein Data Bank (standalone)
  • pdbTools: command line python scripts to manipulate PDB file (standalone)
  • CGRtools: Python Library for Molecule, Reaction and Condensed Graph of Reaction Processing (standalone)
  • PyBioMed: A python package for generating various molecular representations for chemicals, proteins, DNAs and their interactions (standalone)
  • ChemmineR (descriptors, QSAR, etc) standalone
  • RStudio: (standalone)
  • Weka(standalone)
  • CDK (descriptors, QSAR, etc)(standalone)
  • RDKIT (descriptors, QSAR, etc)(standalone)
  • Biopython: freely available tools for biological computation written in Python like text mining in PubMed, sequences, manipulate PDB files, etc (standalone)
  • WebMD: patient forum for text mining and list of drugs, side effects, overdose, images… (online)
  • Chempy (descriptors, QSAR, etc)(standalone)
  • E-Dragon: (descriptors, QSAR, etc, standalone and online)
  • Python.org: Learning python and more (training)
  • scikit-learn: machine learning in Python (standalone)
  • PubChemPy: provides a way to interact with PubChem in Python (standalone)
  • Pycharm: IDE (Integrated Development Environment) for Python (standalone)
  • Reticulate: R interface to Python (standalone)
  • PaDEL: (descriptors, QSAR, etc, standalone and online)
  • ProtDCal :descriptors for sequences and protein 3D-structures (online)
  • Rapidminer: Data science - machine learning (standalone)
  • Orange: Data science - machine learning (standalone)
  • scikit-learn: Machine Learning in Python (standalone)
  • ChemMine: Chemical clustering and analysis, descriptors (online)
  • ChemmineR: Cheminformatics Toolkit for R, descriptors (standalone)
  • ChemBioServer: Chemical clustering, descriptors (online)
  • iFeature (a python package and web server for features extraction and selection from protein and peptide sequences) (online)
  • PubMedMineR: R package with text-mining algorithms to analyze PubMed abstracts (standalone)
  • Carrot2: Open Source Results Clustering Engine that can automatically organise search results into topics. Carrot2 can query PubMed and allows boolean searching. DataViz (online)
  • VOSViewer: tool for constructing and visualising bibliometric networks based on journals, researchers or individual publications. DataViz (standalone)
  • Voyant: web-based text analysis tool with a variety of functions. Search results from databases can be uploaded to the tool to show word frequency, words in phrases and word trending. DataViz (online)
  • Text analyser: Drag and drop full text articles and the tool will analyse the text and identify the key topics. DataViz (online)
  • PolySearch2: text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more (online)
  • BioReader: Text mining and classification on pubmed abstract (online)
  • PubReMiner: When you submit your query (which can be any query that can be processed by PubMed), PubReMiner will process the result of that query and display its results in frequency tables, which can be added/excluded from the query to optimize the results (online)
  • Medline Ranker: Text classification (online)
  • BioSeq-Analysis 2.0: analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches (online and standalone)
  • Mold2 (descriptors from a two-dimensional chemical structure) (standalone)
  • PyDPI: Freely Available Python Package for Chemoinformatics, Bioinformatics, and Chemogenomics Studies (descriptors proteins, ligands, computation of fingerprints...) (standalone)
  • NetGO: improving large-scale protein function prediction with massive network information (online)
  • Pergola-web: web server for the visualization and analysis of longitudinal behavioral data using repurposed genomics tools and standards (dataviz, online) (online)
  • ActLSmaps: Activity Landscape Plotter: A Web-Based Application for the Analysis of Structure–Activity Relationships (online)
  • Data Retrieval Knime: A new semi-automated workflow for chemical data retrieval and quality checking for modeling applications (knime) (standalone)
  • ResponseNet V3: revealing signaling and regulatory pathways connecting your proteins and genes across human tissues (online)
  • VOLPES: an interactive web-based tool for visualizing and comparing physicochemical properties of biological sequences, descriptors (online)
  • web-rMKL: a web server for dimensionality reduction and sample clustering of multi-view data based on unsupervised multiple kernel learning (online)
  • VOLPES: an interactive web-based tool for visualizing and comparing physicochemical properties of biological sequences, descriptors (online)
  • BEERE: server for biomedical entity expansion, ranking and explorations (online)
  • stitch: Chemical-Protein Interaction Networks (online)
  • PubTator central: automated concept annotation for biomedical full text articles, text mining (online)
  • PathMe: merging and exploring mechanistic pathway knowledge. Allows users to comprehensively explore pathway crosstalk and compare areas of consensus and discrepancies (python, standalone and online)
  • 3D-e-Chem Nodes for KNIME: The nodes complement existing cheminformatics and bioinformatics nodes to enable the efficient exploitation of structural and pharmacological protein-ligand interaction data from proteome-wide databases (including kinases, GPCRs…) (standalone)
  • CD-HIT: clustering and comparing protein or nucleotide sequences (redundant sequences... for machine learning...) (online)
  • TeachOpenCADD KNIME workflows: teaching chemoinformatics with Knime, also available via Jupyter Notebooks, but RDKIT requires, good luck with the installation of RDKIT some some OS (standalone)
  • COVER: Conformational Oversampling as Data Augmentation for Molecules (standalone)
  • RESOLVED2: Prediction of Drug Approval After Phase I Clinical Trials in Oncology (online)
  • rstoolbox: a Python library for large-scale analysis of computational protein design data and structural bioinformatics (standalone)

Other directories of tools

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© Bruno Villoutreix. A first version of this Website was launched in 2006. Thank to Natacha Oliveira