Shortlist


If VLS3D is useful for your research (last update Oct 18, 2018)
Please cite: Villoutreix et al. Drug Discovery Today 2013, 18:1081-9

 

 

2D molecular visualization (chemicals & proteins)

  • LeView: protein-ligand (standalone)
  • PoseView: protein-ligand (online)
  • C-SPADE: web-application serves as an interactive and innovative visualization tool for drug screening data (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)
  • 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)
  • Rocker (ROC curve visualization) (online and standalone)
  • ChemCom (compare compounds) (standalone)
  • GPU-Accelerated Compound Library Comparison (Microsoft Windows platform) (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 (online 3D or 2D)

  • Multiple sequence alignment (MSA): alignment of three or more biological sequences (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)
  • 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)
  • 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)
  • ChimeraX: (standalone)
  • WebMO: free World Wide Web-based interface to computational chemistry packages (standalone)
  • 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) (standalone)
  • 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)
  • HMMER: biosequence analysis using profile hidden Markov models (standalone)
  • HMMER: (online)
  • ProtDec-LTR: protein remote homology detection (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)
  • LoopIng: method based on the Random Forest automatic learning technique, designed to select structural templates for protein loops (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)
  • LOMETS: Local Meta-Threading-Server web service for protein structure prediction (online)
  • HOMCOS: HOMology modeling of COmplex Structure (online)
  • ProFold: web server for protein fold classification (online)
  • PROTEUS2: web server designed to support comprehensive protein structure prediction and structure-based annotation (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)
  • REStLESS: Automated Translation of Glycan Sequences from Residue-Based Notation to SMILES and Atomic Coordinates (online)
  • Glycomics@ExPASy: glycoinformatics (online)
  • UniCarbKB: online information storage and search platform for glycomics, carbohydrates and glycobiology research (online)
  • 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)
  • AbDesigner3D: a structure-guided tool for peptide-based antibody production (online)
  • BRepertoire: a user-friendly web server for analysing antibody repertoire data (online)
  • Third hypervariable loop: dataset (standalone)
  • Rosetta Antibody (online)
  • DIGIT: database of immunoglobulin variable domain sequences annotated with the type of antigen (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)
  • 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)
  • 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)
  • GWIDD: genome wide docking database (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)
  • 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)
  • PubAngioGen (cancer) (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)
  • MoRFpred: Predicting Functions of Disordered Proteins, input sequence (online)
  • PPInS: a repository of protein-protein interaction sitesbase, input a PDB code (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)
  • 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)
  • 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: structural analysis...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

Molecular simulation - refinement - flexibility (macromolecules)

  • Chiron minimizes steric clashes using short discrete molecular dynamics(DMD) simulations
  • Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Polarizable Force Fields
  • 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)
  • Naccess: calculates the accessible area of a molecule from a PDB file
  • FreeSASA: calculates the accessible area of molecules, different chains, etc
  • iFold for interactive protein folding/unfolding simulations
  • 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. Standalone scripts also available)
  • Abalone
  • AQUASOL predict water binding sites
  • VLDP can also be used to add water online
  • Princeton_TIGRESS
  • PreFRP
  • 3Drefine
  • ModRefiner
  • FG-MD
  • NOMAD-ref
  • iMODS
  • WEBnma
  • MDWeb
  • Gromacs
  • AMBER
  • CHARMM
  • CHARMM-GUI (eg solvator to add water molecules...)
  • DynOmics (dynamics of structural proteome)
  • Amber tools
  • YASARA dynamics
  • GROMITA-GUI (GROMACS)
  • FireProt: automated design of thermostable proteins
  • ReFOLD (Refinement of 3D protein models)
  • SEEKR (scripts for ligand-receptor kinetic calculations)
  • NWChem: High-Performance Computational Chemistry
  • MCTBI: metal ion effects in RNA structures
  • SimRNAweb (simulation RNA)
  • 3D-NuS (simulation non-canonical 3-Dimensional Nucleic Acid Structures)
  • CHARMM-GUI
  • FlexPred
  • SPECTRUS
  • Bio3D-web NMA: normal mode analysis of protein structures (elastic network models (ENMs), residue fluctuations, mode visualization...
  • LipidBuilder
  • HTMD

Electrostatics of macromolecules

  • Bluues: Electrostatic properties of proteins based on generalized Born radii (online)
  • 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)
  • 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)
  • 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)
  • 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: 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 (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)
  • LISE: Ligand Binding Site Prediction Using Ligand Interacting and Binding Site-Enriched Protein Triangles (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 (protein-ligand interaction 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)
  • GIRAF (pocket comparison online)
  • Imaaagine (pocket comparison online)
  • IsoCleft (pocket comparison online)
  • LabelHash (pocket comparison online)
  • PDBSITE / PDBsitescan (pocket comparison online)
  • pevoSOAR (pocket comparison online)
  • PINTS (pocket comparison online)
  • PocketAlign (pocket comparison online)
  • PocketMatch (pocket comparison online)
  • SeSAW (pocket comparison online)
  • SiteBinder (pocket comparison standalone)
  • 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)
  • IsoMIF Finder (pocket comparison, field) (standalone)
  • 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)
  • Dowser++ (water - hydrate)
  • 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 databases

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

  • Genomic Position to Protein Sequence and 3D Structure at the PDB
  • Interactome INSIDER: a structural interactome browser for genomic studies
  • TKSA-MC: A Web Server for rational mutation through the optimization of protein charge interactions (Tanford-Kirkwood Surface Accessibility model) (standalone on GitHub)
  • MolArt: MOLecular STructure AnnotatoR, enables users to view annotated protein sequence (including variation data from large scale studies) and overlay the annotations over a corresponding experimental or predicted protein structure
  • VarAFT: disease-causing variants annotation
  • ELASPIC: proteome-wide structure-based prediction of mutation effects on protein stability and binding affinity (online)
  • MoRFpred: Predicting Functions of Disordered Proteins (online)
  • 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)
  • SNPdryad (Deleterious Non-Synonymous SNP Predictions for Human, sequence)
  • 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
  • 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
  • DUET: stability change by combining two approaches
  • CUPSAT Structure based (stability change)
  • Eris 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
  • MutPred Sequence 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)
  • GenomeRunner
  • Cancer3D
  • MANORAA
  • mCSM-lig
  • Virtual Pharmacist
  • 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
  • Interpretome
  • 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)
  • Amino Acid Interaction (INTAA) - structural analysis
  • 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-NA: (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): prediction of aggregation (proteins)
  • Protter (interactive protein feature visualization)
  • 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

3D structure prediction for small chemical compounds

  • Cosmos (online)
  • Spores (check structure, protonation, standalone)
  • Chemaxon: (standalone)
  • Balloon: (standalone)
  • Frog2 (standalone and online)
  • DataWarrior (standalone)
  • Chemozart (3D molecule editor online)
  • Knodle (standalone automatic perception)
  • Ambitcli (no 3D but Java application for standardization) (standalone)
  • 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

Ligand-based virtual screening & de novo design

ADME-Tox

  • hERG: hERG prediction model (input smiles), online
  • hERGdb: integrated database for hERG blocking small molecules and predictions (on the way) (online)
  • Pred-hERG: machine learning to predict hERG (online)
  • 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)
  • ADMETlab: Systematic ADMET evaluation based on a comprehensively collected ADMET database (numerous models, Caco-2, Pgp, Skin, Ames, DILI....) online, input smiles or SDF
  • 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)
  • 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)
  • 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
  • WhichCyp Web Service (WhichCyp predicts which P450 isoform will bind/metabolize a molecule using simple yes/no classification models) (does not seem to run)
  • 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)
  • DemQSAR Online Human Volume of Distribution and Human Clearance (online, input SDF)
  • ChemBioServer: Toxicity Filtering (some Toxicophores) (online)
  • 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)
  • ClinicalTrials.gov: registry of clinical trials (online)
  • WebCSD: the on-line portal to the Cambridge Structural Database (CSD), small molecule experimental 3D structures (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)
  • 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)
  • 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
  • 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
  • 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)
  • Protein Data Bank (PDB: many tools and search utilities)
  • 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
  • DrugCentral
  • 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
  • Chembl
  • PubChem
  • Fetch PubChem compounds
  • Fetch PubChem compounds with Ligdig
  • Chebi
  • KEGG ligand
  • PDBeChem
  • HEDD the human epigenetic drug database
  • NPC Pharmaceutical Collection
  • Zinc
  • Molport
  • eMolecules
  • ChemSpider
  • BioLiP
  • TTD
  • SWEETLEAD
  • DCDB (drug combination database)
  • SuperTarget
  • Matador
  • PLIC
  • PoSSuM (pocket comparison online)
  • ProBis: pocket comparison online
  • sc-PDB
  • PDB
  • PDBe
  • Credo
  • PDBbind
  • PLI
  • FDALabel
  • Binding DB
  • Wikipedia chemical structure explorer: online
  • BioGRID
  • MTLD (Multiple target)
  • HerDing (herb to treat diseases)
  • SBKB
  • Pharos (druggable genome)
  • OpenTargets platform
  • Binding MOAD
  • OpenTargets
  • DGIdb (Drug gene interactions database)
  • Pharos (druggable genome - TCRD)
  • DTO (drug target ontology)
  • Pharos Pubmed Score (PMScore)
  • 3did
  • TCRD database
  • PharmGKB
  • Collection of drugs Illuminating the druggable genome
  • The IUPHAR/BPS Guide to PHARMACOLOGY
  • Harmonizome: Integrated knowledge about genes and proteins
  • ExCAPE-DB (online)
  • ExCAPE-DB (datasets)
  • Chemical Probes
  • Consensuspathdb
  • Pathguide
  • Cancer Cell Map Initiative (CCMI)
  • DTome
  • Genomics, Evidence, Neoplasia, Information, Exchange (GENIE)
  • Genomics Data Miner (GMine)
  • 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)
    SMMRNA: a database of small molecule modulators of RNA
  • DrugKiNET (kinase inhibitors)
  • Nucleic acid ligand database (NALDB)
  • Probes & Drugs portal

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

Other directories of tools

  • Last updated on .

Email

bruno.villoutreix(at)gmail.com

Address

Follow me


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