List of in silico drug design online services, standalone and related databases by Dr. B. Villoutreix, research director at the French National Medical Research Institute (Inserm). Update May 23, 2013. 1478 Weblinks
Patent search (Section 1)
Chemistry toolkits, biostats, utilities (Section 2)
Displaying molecules/sequences, Visualization & some commercial tools (Section 3)
Compound collections, bioisosteres, databases...(Section 4)
QSAR, descriptors and related (Section 5)
File Formats (Section 6)
ADMET predictions & databases (Section 7)
Off-targets, polypharmacology, ADRs, prediction of bioactivity, profiling (Section 8)
Targets & Target-ligand complexes (Section 9)
3D structure generator for small molecules (Section 10)
Homology modeling, structural bioinformatics (Section 11)
Protein docking, PPI, hot spot (Section 12)
Molecular simulation & electrostatics (Section 13)
Virtual screening & related (eg, some aspects of chemical space) (Section 14)
Binding pocket, druggability (Section 15)
Mutations (Section 16)
Peptides, antibodies, epitopes (Section 17, see also section 11)
Modeling loops (Section 18, also sections 11 and 13)
Teaching & Training, Tutorials (Section 19)
Other links (e.g., Open innovation in drug discovery...)(Section 20)
3d adme-tox analysis available drug design binding chemical chemistry collection compound computational data database datasets design docking drug free functional information interaction interface ligand link modeling molecular molecules mutations online drug discovery peptides prediction patent properties protein-protein packages modulators scoring screening quality by design sequences server sites software drug structures targets in silico tools tox webtool
created at TagCrowd.com

Patents

LINK Inpi

LINK Espacenet

LINK Surechem: Allows for structural search using SMILES

LINK European patent office

LINK Duke

LINK United States Patent

LINK Google patents

LINK WIPO

LINK to organic-reaction.com, overview of recent patents

LINK the annotation-enriched non-redundant patent sequence database

LINK the complement patent database

LINK SCRIPDB Search for a molecule in US Patents 2001-2011


URLs Binding pocket prediction & comparison Comments
LINK EPOS_BP : Ensemble of Pockets on Protein Surfaces with BALLPass standalone
LINK FINDSITE is a threading-based binding site prediction/protein functional inference/ligand screening algorithm that detects common ligand binding sites in a set of evolutionarily related proteins. Crystal structures as well as protein models can be used as the target structures online pocket detection
LINK AutoMatch: target-binding protein design and enzyme design by automatic pinpointing potential active sites in available protein scaffolds standalone
LINK The FunFOLD Binding Site Residue Prediction Server: predicts likely ligand binding site residues for a submitted amino acid sequence online binding zone
LINK APoc: Large scale identification of similar protein pockets software is freely available to ALL users, compare pockets
LINK TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins data
LINK LISE: Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles online
LINK MolLoc is a web server for the comparison of molecular surfaces online
LINK PESDserv Compare binding sites of proteins online
LINK pevoSOAR detects functional pockets of proteins based on structural and residue substitution pattern similarities between a pocket or void on the query protein to a database of enzyme family representative functional pockets online
LINK PocketAlign: Comparison of binding sites online
LINK POOL server: machine learning application for functional site prediction in proteins online
LINK CHED predicts 3D intra-chain protein binding sites for transition metals (Zn, Fe, Mn, Cu, Ni, Co, and Ca and Mg sites that can be replaced by a transition metal online
LINK MetalDetector predicts metal binding sites in proteins using sequence information alone. Prediction is limited to transition metals (with the addition of heme and Fe/S clusters) and to CYS and HIS online
LINK SOAK: Metal ion binding sites, affinities, and specificities from structure online
LINK PLATINUM is designed for calculation of hydrophobic properties of molecules and their match or mismatch in receptor-ligand complexes. These properties may help to analyze results of molecular docking online
LINK PINUP: Protein binding site prediction with an empirical scoring function online
LINK ANCHOR seeks to identify segments that reside in disordered regions, cannot form enough favorable intrachain interactions to fold on their own and are likely to gain stabilizing energy by interacting with a globular protein partner online
LINK FTMap: Computational solvent mapping is a powerful tool to understand interactions between proteins and solvent molecules. It docks small organic molecules on a protein surface, finds favorable binding positions, clusters the conformations of all prediction, and ranks the clusters on the basis of their average free energy. The low energy clusters are grouped into consensus sites and the largest consensus sites are able to identify actice or ligand binding sites. The docked fragments can also be served as the building blocks for fragment-based drug design online
LINK FTProd: binding site comparison across multiple structures standalone
LINK SiMMap for inferring site-moiety map to recognize interaction preferences between protein pockets and compound moieties online
LINK CAVER is a software tool for analysis and visualisation of channels (tunnels) in protein structures online and standalone
LINK 3V (Voss volume voxelator): Web tool for volume calculation online
LINK Protein frustratometer: a tool to localize energetic frustration in protein molecules. Frustration is a useful concept for gaining insight to the proteins biological behavior by analyzing how the energy is distributed in protein structures and how mutations or conformational changes shift the energetics. Sites of high local frustration often indicate biologically important regions involved in binding or allostery. In contrast, minimally frustrated linkages comprise a stable folding core of the molecule that is conserved in conformational changes online analysis
LINK aCSM: noise-free graph-based signatures to large-scale receptor-based ligand prediction standalone, it seems the link provided by the authors does not work, thus contact directly, paper in Bioinformatics 2013, Pires DE et al
LINK Pocket V2: A method for deducing receptor-based pharmacophore standalone
LINK AutoMap: A tool for analyzing protein-ligand recognition using multiple ligand binding modes standalone
LINK EzyPred: A top-down approach for predicting enzyme functional classes and sub-classes online
LINK EnzClassPred at Bio-AIMS: Enzyme Class Prediction online
LINK AADS: Active Site Prediction of Protein server computes the cavities in a given protein online
LINK Fpocket: find pocket - geometry-based standalone
LINK FuzCav, alignment-free high-throughput algorithm to compute pairwise similarities between protein-ligand binding sites online
LINK Structure-based DrugEBIlity: Users can survey different types of druggability scores of a given protein structure online
LINK IFP, interaction fingerprint, Generates interaction fingerprint for a protein/ligand complex online
LINK Shaper: Align and scores negative binding site images, Desaphy et al, 2012, Comparison and Druggability Prediction of Protein-Ligand Binding Sites from Pharmacophore-Annotated Cavity Shapes online
LINK SiteAlign: Align and compare druggable protein sites online
LINK VolSite: Generates negative images of binding sites encoding both shape and pharmacophoric properties at regularly spaced grid points online
LINK fpocket, see also MDpocket (Pocket detection on MD trajectories), hpocket (Pocket detection on homologous structures)...online online
LINK Ghecom: A program for finding multi-scale pockets on protein surfaces using mathematical morphology online
LINK LigSite csc: find pockets online
LINK SCREEN2 find pockets and gives descriptors online
LINK FunFOLDQA standalone
LINK StrucTools is a set of tools commonly used for structural biology calculations with PDB files online, structural analysis
LINK ConSurf: enables the identification of functionally important regions on the surface of a protein or domain, of known three-dimensional (3D) structure, based on the phylogenetic relations between its close sequence homologues online
LINK Rate4Site: detects conserved amino-acid sites by computing the relative evolutionary rate for each site in the multiple sequence alignment standalone
LINK PASS find pockets standalone
LINK Voidoo: detection of cavities standalone
LINK SurfNet: calculation of clefts in protein surfaces standalone
LINK ProBiS: Pocket detection & comparison online
LINK McVol: Compute the Volume of Proteins and finding internal cavities standalone
LINK EPOS_BP - Ensemble of Pockets on Protein Surfaces with BALLPass (PASS algorithm was re-implemented) standalone
LINK PoSSuM Database, pocket similarity search (searches for 3.4 million known and potential binding sites...) online
LINK PocketAnalyzerPCA: combines a geometric algorithm for detecting pockets in proteins with Principal Component Analysis and clustering. This enables visualization and analysis of pocket conformational distributions of large sets of protein structures standalone
LINK Mode of Action by NeTwoRk Analysis (MANTRA) is a 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
LINK DvD: An R and Cytoscape plug-in for comparing Drug and Disease profiles standalone
LINK FINDSITEcomb: A threading/structure-based, proteomic-scale virtual ligand screening approach online
LINK SiteHound and EasyMIFs, dentifies protein regions that are likely to interact with ligands standalone
LINK Protein-ligand specificity: Discovering Rules for protein-ligand specificity using support vector inductive logic programming standalone
LINK Qhull computes the convex hull, Delaunay triangulation... standalone
LINK Q-site and Pocketfinder (geometry and energy-based) online
LINK Pocketfinder online
LINK CASTp: Binding sites and active sites of proteins and DNAs online and standalone
LINK PRIDE2 server calculates the PRobability of IDEntity between three-dimensional domains (or whole structures) and offer varied various compararisons with known structures online, structural analysis
LINK PDBeMotif search tool that facilitates exploration of the Protein Data Bank (PDB) by combining protein sequence, chemical structure and 3D data in a single search online, structural analysis of pockets
LINK PDBeMotif Motifs and binding Sites, other URL online
LINK SMAP is designed for the comparison of protein 3D motifs independent on the sequence order online
LINK MolAxis Efficient and Accurate Identification of Channels in Macromolecules online
LINK PocketDepth find pockets online
LINK Erebus: Identifying the location of binding sites on proteins online
LINK PROSURFER: contains information about structural similarities with respect to the query surfaces. Also 249 ligand-binding sites from the MDL Drug Data Report (MDDR) database online
LINK AutoLigand, can find binding pockets standalone
LINK Superimpose is a framework for superposition - from protein structure alignment to in silico screening online
LINK fPOP (footprinting Pockets Of Proteins), protein binding site comparison online
LINK SMAP-WS: comparison and similarity search online
LINK PROtein SURFace ExploreR online
LINK 3DLigandSite: prediction of ligand binding sites, Users can either submit a sequence or a protein structure online
LINK Pocketannotate: functional annotation of proteins online
LINK PocketQuery is a web service for interactively exploring hot regions online
LINK PASS online
LINK Active Site Prediction of Protein online
LINK SiteComp provides 3 major types of binding site analysis online
LINK ConCavity online and standalone
LINK MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels online
LINK SLITHER A web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating across membrane transporters online
LINK Cavitor, find pockets This software is freely available
LINK PocketPicker, available as a Pymol plugin standalone
LINK Pymlp (Molecular Lipophilicity Potential evaluator) calculates lipophilicity potential maps of protein standalone
LINK Tools to analyze protein surface...protein fingerprint, to dock proteins... standalone and some online
LINK DMS: computes molecular surface open source program written in C, standalone
LINK MSMS: molecular surface and others standalone
LINK GETAREA 1.1: Solvent Accessible Surface Areas online
LINK Pocasa: POcket-CAvity Search Application online
LINK POVME: measure binding-pocket volumes standalone
LINK CPASS - Comparison of Protein Active-Site Structures run from a simple web-based entry form (password protected) and requires 18-24 hours to complete, online
LINK eF-seek: protein binding site comparison online
LINK eF-site: electrostatic surface of functional site online
LINK SplitPocket online
LINK MetaPocket online
LINK DoGSiteScorer: binding site prediction, druggability assessment online
LINK SuperStar tool for analysis of binding sites standalone
LINK SiteEngines Functional Sites Structural Search, recognizes regions on the surface of one protein that resemble a specific binding site of another online
LINK PDBSiteScan automatically performs the best superposition of sites online
LINK PINTS finds reoccuring three-dimensional patterns of amino acids online
LINK Multibind: Multiple Alignment of Protein Binding Sites online
LINK PESDserv: Compare binding sites of proteins online
LINK SUMO: Tools for the analysis of binding sites and to find similar motifs online
LINK RNABindR v2.0: analyzes and predicts RNA-binding sites in proteins online
LINK PAR-3D: predicts protein active site residues online
LINK PDTD: a web-accessible protein database for drug target identification online, about 1200 binding pockets
LINK BioDrugScreen online, About 1920 binding pockets
LINK SePreSA A drug molecule is submitted to the server and its potential interaction with multiple adverse drug reaction targets is calculated using DOCK program Small molecule docking, About 115 pockets, online
LINK DRAR-CPI: drug repositioning and adverse drug reaction about 385 binding pocket, online
LINK About 2900 binding pockets to dowload (Li YY, An J, Jones SJ, A computational approach to finding novel targets for existing drugs, PLoS Comput Biol. 2011) dataset
LINK Sc-PDB: tool for analysis of binding sites, database of about 10000 binding pockets online binding pockets and standalone
LINK Pdbfun identification of local structural similarities online
LINK SimDOCK: Ligand transposition server online
LINK Docking with substructure query in a protein family online
LINK The ProFunc server help identify the biochemical function of a protein online, structural analysis
LINK eF-Site Electrostatic surface of functional sites online
LINK proSAT2 : Features for visualizing SwissProt and PROSITE functional annotations online
LINK FeatureMap3D: map protein features such as post-translational modifications, protease cleavage sites or exonic structure onto 3D structures of homologous proteins online
LINK ProKware: Integrated system containing interactive graphic interface and abundant protein property annotations a the structural level online
LINK Protemot: server that carries out prediction of protein binding sites online
LINK The SARIG Server: Structural Analysis of Residue Interaction Graphs online
LINK KBDOCK is a 3D database system that defines and spatially clusters protein binding sites for knowledge-based protein docking online
LINK DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins online
LINK POOL server: machine learning application for functional site prediction in proteins online
LINK CrystalDock Computer algorithm that aids the computational identification of molecular fragments predicted to bind a receptor pocket of interest standalone
LINK Pepsite2: Prediction of peptide binding sites on protein surfaces online
Pocket databases and related
LINK Drug-like Density: A Method of Quantifying the Bindability of a Protein Target Based on a Very Large Set of Pockets and Drug-like Ligands from the Protein Data Bank Sheridan et al., J. Chem. Inf. Model., 2010, 50, pp 2029. About 5000 drug-like ligands from the PDB in SDF you have to get the publication, dataset
LINK DCD binding pocket database to validate packages predicting druggability annotated list of proteins, dataset
LINK PSCDB: a database for protein structural change upon ligand binding online database
LINK Apo and holo protein dataset dataset
LINK The Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the PDB database
LINK PDBSite: a database on protein active sites and their spatial environment database
LINK SitesBase: database of ligand binding sites, can compare binding pockets online
LINK The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure (previously PROCAT) database
LINK LigASite database of binding sites: proteins with one unbound structure and at least one structure of the protein-ligand complex .
LINK The SuperSite is an encyclopedia that is dedicated to a ligand and binding site oriented view of the protein structural space database
LINK PocketAnnotate: Non-Redundant Binding Site Database, can compare pockets with PocketMatch database

URLs Chemistry toolkits, utilities Comments
LINK CADD Group Chemoinformatics Tools and User Services online tools for chemistry
LINK The Chemistry Toolkit Rosetta is a wiki for sharing how to use different chemistry toolkits for the same set of common tasks online information
LINK The ROCR is an R package for evaluating and visualizing classifier performance online, server is down?
LINK The ROCR is an R package for evaluating and visualizing classifier performance with only 3 commands standalone
LINK ScrumPy Metabolic Modelling in Python .
LINK This service works as a resolver for different chemical structure identifiers and allows one to convert a given structure identifier into another representation or structure identifier. It can help you identify and find the chemical structure if you have an identifier such as an InChIKey online
LINK Chemical Translation Service online
LINK ChemSpot is a named entity recognition tool (standalone) standalone
LINK OPSIN: Open Parser for Systematic IUPAC nomenclature .
LINK Compounds In Literature (Pharmaceutical Bioinformatics) Search for compound name, InChI or SMILES online
LINK DAKOTA A Multilevel Parallel Object-Oriented Framework for Design Optimization, Parameter Estimation, Uncertainty Quantification, and Sensitivity Analysis standalone
LINK ChemToolBox contains several internal databases that assist lab work standalone
LINK PrecisionTree .
LINK C4.5 .
LINK C5.0 .
LINK k Nearest Neighbor .
LINK Neural network .
LINK Neural network: JATOON .
LINK Neural network: JATOON .
LINK NeuroShell Predictor .
LINK SVM .
LINK SVM .
LINK Generates Kohonen's Self-Organizing Maps online .
LINK learn about computer clusters Training about computer clusters
LINK Condor Tools to speed-up computations - grid - fast computations - computing
LINK OpenMolGrid: tools to speed-up computations Tools to speed-up computations
LINK rggobi is an R package that provides an easy interface with GGobi Biostatistics - R interface
LINK SLIMS is a laboratory information management system Chemical data storage - database
LINK Weka 3: Data Mining Software in Java Data Mining Software
LINK The Chemical Descriptors Library (CDL) is a C++ library that provides functionality in the area of chemical informatics Molecular Descriptors
LINK Open source clustering software Clustering
LINK Clustering software. SUBSET Clustering
LINK The web-based RESP ESP charge DataBase is a free and new source of RESP and ESP atomic charge values and force field libraries for model systems and/or small molecules Chemistry tools - Online
LINK Aten: is a tool for computational chemists, molecular dynamicists. It does: Build and edit atomic coordinates, Generate superstructures from crystal information Chemistry tools, standalone
LINK Vega WE : Web server for file translation tool, properties and surface calculation Chemistry tools, online
LINK the babel package online: BabelWeb Chemistry tools - toolkit - chemoinformatics, online
LINK Many chemoinformatics tools - Prof Alexandre Varnek lab = ISIDA, fragmentor...etc Chemistry tools - toolkit - chemoinformatics, some are online, others are standalone
LINK Mol2 file format
(2D or 3D)		 Mol2 format
(Chemistry)
LINK The Protein Data
Bank, see section describing the PDB format
(Deshpande et al.
2005)		 Macro-molecule 3D
structures

LINK

LINK

 OpenBabel: File format conversion Chemistry tools
LINK Chemistry toolkit - perlmol Chemistry tools, standalone
LINK GIF/PNG-creator with SMILES input Compound drawing, online

LINK

LINK

 Computational chemistry package - JOElib Chemistry tools, standalone
LINK Computational chemistry package: Ghemical Chemistry tools, standalone
LINK Computer tools for chemistry, ADME-tox....Marvin is a suite of Java based chemistry software that have different forms: Marvin Applets, Marvin Beans, MarvinSketch Chemistry tools, standalone
LINK CDK: Chemistry development kit (Steinbeck et al. 2006) Chemistry tools, standalone
LINK Chemistry toolkit - frowns Chemistry tools, standalone
LINK A C++ toolbox for chemoinformatics Mahe et al. 2005 Chemistry tools, standalone
LINK SketchEI: Chemical structure sketching tool Compound drawing, standalone
LINK cactus: Online SMILES translator and structure generator Compound drawing, online
LINK RDKit: Cheminformatics and Machine Learning Software Chemistry tools, standalone
LINK The SDF toolkit (in Perl) essentially for small molecules Chemistry tools, standalone
LINK Moloc: Roche Biostructural modeling package for small and large molecules. This package seems free but ? Chemistry tools, standalone
LINK MayaChemTools is a growing collection of Perl scripts to support day-to-day computational discovery needs... Chemistry tools, standalone
LINK A Java Chemical Structure Editor Compound drawing, standalone
LINK Information about SDF format SDF format
LINK Vigyaan is an electronic workbench for bioinformatics, computational biology and computational chemistry Different modeling packages
LINK MOPAC (Molecular Orbital PACkage) is a semiempirical quantum chemistry program semiempirical quantum chemistry - ADME since pKa, standalone
LINK Walking the web of chemical informatics, package like Ruby CDK chemistry toolkit Ruby CDK chemistry toolkit and many others
LINK An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP) chemo- and bioinformatics
LINK ChemFileBrowser is a win32 free sotfware for chemistry Some Chemistry tools for windows
LINK Many tools from Andrew C.R. Martin's Bioinformatics group. From mutations to Profit for rmsd computations to sending jobs to cluster Many valuable tools for structural bioinformatics
LINK software, shareware and freeware for Macintosh, Windows and Palm for mac and windows
LINK sourceforge.net chemistry and bioinformatics sourceforge.net
LINK Obviously Linux for Chemistry Linux for Chemistry


URLs ADMET prediction and databases, software to deal with compound collections Comments
Databases, Datasets
LINK TREND ANALYSIS OF A DATABASE OF INTRAVENOUS PHARMACOKINETIC PARAMETERS IN HUMANS FOR 670 DRUG COMPOUNDS by Obach RS, Franco Lombardo and Nigel J. Waters (Drug Metab Dispos. 2008 Jul;36(7):1385-405) dataset (670 molecules)
LINK list of chemistry and tox databases .
LINK QSPR-THESAURUS database: It contains physico-chemical data and models for four classes of compounds (CADASTER) online
LINK ChEMBLSpace is a Java application for the visual exploration and analysis of the chemogenomic space extracted from the ChEMBL database standalone
LINK Ferenczy and Keseru, how fragments are optimized, 2013 dataset of fragments and optimized compounds
LINK Emanuele Perola An Analysis of the Binding Efficiencies of Drugs and Their Leads in Successful Drug Discovery Programs J Med Chem 2010, Supporting Info, leads and corresponding drugs in SDF dataset of lead and optimized leads
LINK The EBI has a developed and maintained a number of protein structure related databases. The Protein Databank in Europe (PDBe) group, within the EBI, is responsible for the deposition and validation of new protein structures online database
LINK Brenda: The Comprehensive Enzyme Information System online database
LINK EnzymeDetector online
LINK Top 200 prescriptions in 2002 (structure and name of the compounds). Prescription drug. Drug Index Prescribed drugs, online
LINK prescription drugs (structure and name of the compounds). Molecule of the month Prescription drugs, online
LINK FDA approved drugs Drugs, online
LINK Chemical databases Chemical search, online
LINK SuperDrug database: contains 2.396 compounds Drug Database, online
LINK Drug@FDA Online
LINK DrugBank, list of drugs, experimental structures... Online
LINK CPI-Predictor : molecular polypharmacology, off-targets and drug repositioning focused on G protein-coupled receptors and kinome online
LINK Drug3k: Prescription drug information for consumers online
LINK Compilation of web sites that offer chemistry databases/search services, data about toxic molecules, hazardous substances, database browser, Enhanced NCI Database Browser 2.1 Compound Database, ADME/Tox
LINK A free database of commercially available solvents searchable by many properties Solvent Database, online
LINK Chembl, database of bioactive molecules online
LINK GOSTAR is an online scientific database product of GVK BIO. It is the largest manually curated SAR database that contains all the Published and Patented inhibitors against most biological targets and their associated SAR data. GOSTAR database contains compounds from both Discovery and Development along with associated SAR, ADME, Toxicity, and Pharmacokinetic Data. The database contains over 6 million inhibitors and over 14.9 million quantitative SAR points screened from around 2.1 million patents and 296,000 journals commercial database
LINK ChemID Plus: chemical name, physical and toxicological properties Compound Database, ADME/Tox, online
LINK 3DMET: A database of 3D structures of natural metabolites. The current version includes most of the natural products of the KEGG COMPOUND collection online
LINK BiGG Database database is a metabolic reconstruction of human metabolism designed for systems biology simulation and metabolic flux balance modeling database
LINK BioSM: a cheminformatics tool that uses known endogenous mammalian biochemical compounds (as scaffolds) and graph matching methods to identify endogenous mammalian biochemical structures in chemical structure space online
LINK MetaboLights : an open access general purpose repository for metabolomics studies and associated meta-data database
LINK Human Metabolome Database: contains information about small molecule metabolites found in the human body, the database (version 3.0) contains 40278 metabolite entries online
LINK The Human Metabolome Library (HML) online
LINK Toxin and Toxin Target Database (T3DB) is a unique bioinformatics resource that combines detailed toxin data with comprehensive toxin target information. See also at this site: (see also at this site: Animal Toxin Database (ATDB), The Toxicology Data Network (TOXNET), The Comparative Toxicogenomics Database (CTD), The Aggregated Computation Toxicology Resource (ACToR), and SuperToxic online
LINK e-Drug3D offers a facility to explore FDA approved drugs online
LINK MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways online
LINK BioMeta is a database of metabolites and metabolic reactions. Its contents are largely based on the KEGG Ligand database. Compared to the KEGG database, a large number of chemical structures have been corrected with respect to constitution and stereochemistry online
LINK KNApSAcK: A Comprehensive Species-Metabolite Relationship Database, compounds are in 3D with curated stereochemistry, natural products online
LINK DailyMed provides high quality information about marketed drugs Prescribed drugs, online
LINK Thd CYPED database integrates information on sequence and structure of cytochrome P450 monooxygenases to facilitate protein engineering CYP450, online
LINK Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on small chemical compounds ChEBI, online
LINK The ADME databases ADMET, online
LINK FragmentStore : a comprehensive database of fragments linking metabolites, toxic molecules and drugs - database possible off-target interactions, online
LINK A database for facilitating the search for drug Absorption, Distribution, Metabolism, Excretion associated proteins. It contains information about known drug ADME associated proteins, functions, similarities, substrates / ligands, tissue distributions, and other properties of the targets. Over 320 proteins Databases ADME/tox, online
LINK ISSTOX Chemical Toxicity Databases Database, online
LINK ADME DB is a database containing the latest and most comprehensive data on interactions of substances with Drug Metabolizing Enzymes and Drug Transporters Databases ADME/tox, online
LINK Distributed Structure-Searchable Toxicity (DSSTox) Database Network (Richard and Williams 2002; Richard et al. 2002). Check also ACToR at http://www.epa.gov/ACToR/ Databases ADME/tox, online
LINK Toxnet: Databases on toxicology, hazardous chemicals, environmental health, and toxic releases, find information about molecules Databases ADME/tox, online
LINK Toxnet, HSDB, Hazardous substances data bank Databases ADME/tox, online
LINK Databases on toxicology, hazardous chemicals, environmental health, and toxic releases Databases ADME/tox, online
LINK Drug-Induced Toxicity Related Proteins: DITOP Databases ADME/tox, online
LINK INCHEM: Chemical Safety Information from Intergovernmental Organizations Databases ADME/tox, online
LINK In order to facilitate drug design, toxic compounds were collected from literature and web sources in the database SuperToxic ADME/tox database, online
LINK SuperCyp: This database contains about 1,170 drugs, 2,785 Cytochrome-Drug interactions and about 1,200 alleles, check also other links there, prodrugs, Phase 2 enzymes, drugs... ADME/tox database, online
LINK SuperHapten: An Immunogenic Compound Database This database contains currently 7257 haptens, 453 commercially available related antibodies and 24 carriers ADME/tox database, online
LINK Toxicoinformatics database at the FDA (application of systems biology to ADME/Tox). See also Leadscope but not free: http://www.leadscope.com/product_info.php?products_id=53 ADME/tox database
LINK DART (Ji et al. 2003), ADME-AP (Sun et al. 2002), TRMP (Zheng et al. 2004), TTD (Chen et al. 2002a): databases for facilitating the search for drug Absorption, Distribution, Metabolism, Excretion associated proteins. Therapeutic Target Database (268 successful targets in TTD in May 2007) Databases for ADME/tox, Toxicity, online
LINK Metabolomics database online
LINK PHYSPROP database, contains chemical structures, names and physical properties for over 25,000 compounds Chemistry database
LINK Chemistry Databases on the Web -- alphabetical list -- and many more ADME tox... Chemistry Databases
LINK Cancer expert system, carcinogenicity..., EPA, datasets, online tools... ADME/tox, carcinogenicity...
LINK The Carcinogenic Potency Database (CPDB). The Database is a unique and widely used international resource of the results of 6540 chronic, long-term animal cancer tests on 1547 chemicals. ADME/tox, carcinogenicity..., online
LINK OpenTox Community site ADME/tox ...
LINK eChemPortal provides free public access to information on properties of chemicals: Physical Chemical Properties Ecotoxicity Environmental Fate and Behaviour Toxicity ADME/tox, database..., online
LINK PK/DB is a free database and predictive service for researches online
LINK chemxseer is an integrated digital library and database allowing for intelligent search of documents in the chemistry domain and data obtained from chemical kinetics online
LINK This database is an attempt to catalog in a convenient, searchable fashion all publicly available information about the identities of mammalian proteins that become covalently adducted by chemically-reactive metabolites of xenobiotic agents including drugs online
LINK admetSAR models & databases: provides the manually curated data for diverse chemicals associated with known Absorption, Distribution, Metabolism, Excretion and Toxicity profiles ADMET, datasets
LINK MetaADEDB databases ADMET, online
LINK MetaADEDB databases ADMET, online
LINK Chemistry blog - melting point... Chemistry blog
LINK C-ChemBench: The Carolina Cheminformatics Workbench (C-ChemBench) is an integrated toolkit developed by the Carolina Exploratory Center for Cheminformatics Research (CECCR) with the support of the National Institutes of Health. Chembench is a free portal that enables researchers to mine available chemical and biological data Chemistry tools, online
LINK Oral administered drugs are mainly absorbed in the small intestine. Here, depending on drug composition and size, absorption can happen through a variety of processes...Drug Discovery with Quantum Pharmaceuticals Blog ADME and drug design
LINK PKKB(PharmacoKinetics Knowledge Base) is the most extensive freely available database for collecting ADME (Absorption, Distribution, Metabolism, and Excretion) and Toxic properties Chemistry tools, datasets
LINK The phospholipidosis dataset of 182 compounds, Lowe et al. Journal of Cheminformatics 2012 4:2 dataset
LINK Phospholipidosis dataset, Mol. Pharmaceutics, 2010, 7 (5), pp 1708-1714 dataset
Manage collections, navigation in the chemical space..., look at SMARTS
LINK CLEVER (chemical library editing, visualizing and enumerating resource) ADME/tox Database, standalone
LINK ChemoPy: freely available python package for computational biology and chemoinformatics, compute descriptors standalone (linux, windows)
LINK SMARTSeditor standalone Mac, linux, windows
LINK looking at SMARTS SMARTS chemoinfo, online
LINK ChemGPS-NP Web - A tool tuned for navigation in biologically relevant chemical space Chemical Space, Chemoinformatics, online
LINK Scaffold Hunter is a JAVA-based cross-platform open source tool Chemical Space, Chemoinformatics, standalone
LINK ScreeningAssistant 2 is a free and open-source desktop software dedicated to store and manage chemical libraries in a local or network-accessible MySQL database, and perform various analysis using simple and advanced chemoinformatics methods. Linux and Windows Tool to prepare collection, standalone
ADMET and physchem predictions and related tools
LINK ToxPredict (associated to OpenTox) online
LINK E. coli toxicity prediction web server based on QSAR models (Faulon's lab) online, need to register
LINK Vega-QSAR.eu tools for qsar prediction of ADMET (ORCHESTRA is an EU project, funded to disseminate recent research on in silico (computer-based) methods for evaluating the toxicity of chemicals, REACH, courses); ANTARES, alternative to animal testing, CAESAR, EC funded project which was specifically dedicated to develop QSAR models for the REACH legislation standalone
LINK The Natural-Product-Likeness scoring system is implemented as Taverna 2.2 workflows, and is available under Creative Commons Attribution-Share Alike 3.0 Unported License at http://www.myexperiment.org/packs/183.html. The present link goes to the executable standalone java package (under Academic Free License) standalone
LINK The HExpoChem server contains information on diverse sources of chemicals with the aim to explore human health risk from diverse chemicals exposure. Five sources of information are considered i.e. drugs, foods, cosmetics, industrial chemicals and human metabolites corresponding of 10183 unique chemicals with bioactivities for 19 483 human proteins.HExpoChem can help in the decision of potential proteins and proteins complexes associated to life-style diseases. It can assist also to the possible cumulative risk of chemicals that interact to a same set of proteins online
LINK DrugMint is the server to predict the druggabilty of a compound. This server has been developed on the basis of difference in descriptors of approved and experimental small molecules. This server will help in knowing the druggable properties of a chemical structure online
LINK SPARC computes pKa, solubility.. online (need to register)
LINK SOMEViz: a web service for site of metabolism estimating and visualizing ADMET, online
LINK Elucidation of chemical-protein interactions (CPI) spectrum ADMET, online
LINK Computational resources for drug discovery: many tools for ADMET and also QSAR, virtual screening... ADMET, links, online
LINK PaDEL-DDPredictor: A software to calculate pharmacodynamics, pharmacokinetics and toxicological properties of compounds ADMET, standalone
LINK PreADME, drug-likeness, ADMET ADMET, standalone
LINK Rejection rules from Lilly Open Innovation Drug Discovery initiative ADMET software, standalone in C
LINK Mcule.com toxicity checker, Searching for substructures commonly found in toxic and promiscuous ligands, Based on more than 100 SMARTS toxic matching rules Online
LINK Mcule.com property calculator for one molecule (Create a physicochemical property profile) Online
LINK QSAR TOOLBOX: Software for grouping chemicals into categories and filling gaps in (eco)toxicity data needed for assessing the hazard of chemicals .
LINK Ecological Structure Activity Relationships (ECOSAR) online
LINK The Open PHACTS Explorer allows multiple sources of publicly-available pharmacological and physicochemical data to be intuitively queried, and makes data provenance accessible at every step .
LINK RS-WebPredictor Predict cytochrome P450 mediated sites of metabolism on drug-like molecules .
LINK ToxCast Screening Chemicals to Predict Toxicity Faster and Better .
LINK DemQSAR: predicting human volume of distribution and clearance of drugs online
LINK Insilicofirst: Try Entering a Chemical into our Toxicity Prediction Software .
LINK FAF-Drugs2 online ADMET filtering server, compound collection preparation, see the link to the user guide just below. At present uses SDF as input, but can take SMILES for instance via the bank-formatter utility. The outputs can be directly piped into other services Online
LINK FAF-Drugs2 online ADMET filtering server, PAINS (molecules that can interfere with assays...see J Baell in J Med Chem)....Lagorce, Villoutreix et al, Bioinformatics 2011 Chemistry tools, this is the user guide
LINK ToxAlerts: a Web server of structural alerts for toxic chemicals and compounds with potential adverse reactions. The database already contains almost 600 structural alerts for such endpoints as mutagenicity, carcinogenicity, skin sensitization, compounds that undergo metabolic activation, and compounds that form reactive metabolites and, thus, can cause adverse reactions, QSAR models can be built online (OCHEM)
LINK DDI-CPI, a server Predicting Drug-Drug Interaction via Chemical-Protein Interactome online
LINK MycPermCheck online tool for permeability prediction of small molecules against Mycobacterium tuberculosis. Basis of the prediction program is a logistic regression model of the physico-chemical properties of permeable substances Chemistry tools, online
LINK Gusar ecotoxicity online
LINK Gusar acute rat toxicity prediction online
LINK ToxiPred: A server for prediction of aqueous toxicity of small chemical molecules in T. pyriformis online
LINK MDRIpred: A webserver for prediction of Inhibitor against Drug Resistant M.Tuberculosis online
LINK ChemBioServer compound filtering (Rule of 5...) online
LINK Filter-it and related, software packages to filter collections and many others, pharmacophore, extract molecular scaffolds, align shape... standalone
LINK Online BBB predictor (Prof Xiang-Qun (Sean) Xie, Pitt.edu) ADMET CNS BBB, online
LINK MetaPred Server predict metabolizing CYP isoform of a drug molecule/substrate, based on SVM models developed using CDK descriptors online
LINK MetaPrint2D metabolic site predictor online
LINK The PPS predicts plausible pathways for microbial degradation of chemical compounds online
LINK ADME Calculator ADME metabolism, online, slow
LINK OSIRIS Property Explorer Physical Property Estimation ADME, online
LINK Physical Property Estimation online
LINK OECD QSAR Toolbox ADME/tox...
LINK Toxtree, the online version is not so stable online
LINK Toxtree Toxtree: application for grouping chemicals and for predicting various types of toxicity based on decision tree approaches. ADME/tox, european REACH..., standalone but also online tools
LINK Lazar (Lazy Structure-Activity Relationships) is a tool for the prediction of toxic activities ADME/tox, rodent carcinogenicity..., online
LINK The VirtualToxLab 3D ADME/tox, carcinogenicity..., online
LINK Bernard Testa's Virtual logP calculator online, VEGAZZ
LINK Web service to estimate toxicological hazard of a chemical structure. Molecules can be drawn, or input by any identifier (CAS, Name, EINECS) or SMILES or InChI or URL of OpenTox compound or dataset online
LINK ACuteTox (the project is done but some information ?) online
LINK DrugLogit: Predicting the probability of a compound being classified as a drug or non-drug, as well as disease category (or organ) classification online
LINK AlogP: Tools to predict logP (with several methods) online
LINK ZINC: some ADME/tox filtering online
LINK Find compound properties - Edetox Chemistry, online
LINK ADME/tox eyesopen, commercial and demo ADME/tox, online
LINK ADME/tox Molinspiration, commercial and demo online
LINK ADME/tox molsoft, commercial and demo online
LINK ADME/tox chemicalize chemaxon online
LINK ADME/tox online molecular-networks online
LINK Checkmol is a command-line utility program which reads molecular structure files in different formats Find chemical groups, standalone
LINK smartsfilter: ADMET filtering (Glaxo, Oprea, Blake, Pains, NMR alert...) Online
LINK FAF-Drugs: ADME/tox online, Check compounds, flag undesirable groups, search for Baell's PAINS Online
LINK XLOGP3: Compute logP Online
LINK The MetaSite has been developed to predict the site of metabolism for substrates of 2C9, 2D6, 3A4, 1A2 and 2C19 cytochromes ADME/tox, commercial
LINK PharmGKB is a knowledge base that captures the relationships between drugs, diseases/phenotypes and genes involved in pharmacokinetics (PK) and pharmacodynamics (PD) ADME/tox; PK/PD, online
LINK Chemical Effects in Biological Systems (CEBS) knowledge base (application of systems biology to ADME/Tox) ADME/tox
LINK Tissue Distribution DB. TissueDistributionDBs, is a repository of tissue distribution profiles for identifying and ranking the genes in the spectrum of tissue specificity based on Expressed Sequence Tags (ESTs). This repository is currently available for several model organisms across animal and plant kingdoms and is fundamentally based on the UniGene database. Tissue distribution of several targets, online
LINK A KNIME workflow with Schrodinger tools to predict interactions with human serum albumin. Michelle Lynn Hall, William L Jorgensen, and Lewis Whitehead, J Chem Inf Model 2013. Automated ligand- and structure-based protocol for in silico prediction of HSA binding serum albumin binding - HSA, online
LINK Evaluation of drug-human serum albumin binding interactions with support vector machine aided online automated docking. Bioinformatics 2011, Zsila et al serum albumin binding - HSA, online
LINK Allows the users to predict whether a given compound is a P-gp substrate and how it binds to and interacts with P-gp Pgp ADMET, online, commercial, allows one compound
LINK SMARTCyp server predicts the sites in molecules that are most liable to cytochrome P450 mediated metabolism CYP450, online
LINK IMPACTS: A program for the prediction of the sites of metabolism (SOM) of drugs in CYP P450 proteins based on docking and transition states CYP450, standalone
LINK Ursu O, Oprea TI. http://www.softconference.com/ACSchem/player.asp?PVQ=GLHF&fVQ=FFIIKF&hVQ= Model-free drug-likeness from fragments. http://pasilla.health.unm.edu/tomcat/drug-likeness/ J Chem Inf Model. 2010 Aug 23;50(8):1387-94. drug-likeness
LINK Jim Empfield - physchem and drug - 2010 talk Seminar
LINK Directory of computer-aided Drug Design tools Drug Design tools
LINK Pathguide contains information about 325 biological pathway related resources and molecular interaction related resources including Protein-Protein Interactions and many others A pathway resource list
LINK Free software and code for public use NIH Chemical Genomics Center
LINK In Greek mythology, ADMETUS was a king of Pherae in Thessaly who is famed for his hospitality and justice. Here, ADMETUS referred to ADME/T UtilitieS ADMET, online
LINK the official database of the IUPHAR Committee on Receptor Nomenclature and Drug Classification. Incorporating detailed pharmacological, functional and pathophysiological information on G Protein-Coupled Receptors, Voltage-Gated Ion Channels, Ligand-Gated Ion Channels and Nuclear Hormone Receptors online
LINK PASS Inet 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. off-target, tox...online
LINK Modeling chemical mutagenicity. Langham JJ, Jain AN. J Chem Inf Model. 2008 48:1833-9. Contact the authors ADMET-software


URLs Compound collections and or compound-macromolecule data Comments
LINK Collection for FBDD/FBLD : commercial fragments (privileged strutures) extracted from FDA approved drugs .
LINK BitterDB a database of about 570 bitter compounds database online
LINK StreptomeDB: a resource for natural compounds isolated from Streptomyces species database
LINK NPACT: Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database database
LINK UNPD universal natural products database in May 2013, about 197201 natural products from plants, animals and microorganisms database
LINK KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms database
LINK CBLigand.org or CBID is a Web-interfaced cannabinoid molecular information database repository that are designed and constructed to facility data-sharing and information exchange among scientific research communities with online structure search functions and data analysis tools implemented online
LINK CamMedNP: Building the Cameroonian 3D structural natural products database for virtual screening, Fidele Ntie-Kang et al., BMC Complementary and Alternative Medicine 2013, contact the authors and check the supplement file. Over 2500 molecules database
LINK Xemistry: Interactive Quantitative Structure Fragmentation online
LINK Xemistry: Chemical Structure Algorithm consistency verification service online
LINK Chemistry database on the web online, many information can be found there
LINK SciFinder provides researchers with unlimited access to the world s largest and most reliable collection of chemistry and related science information online, commercial
LINK ScreeningAssistant 2 is a free and open-source desktop software dedicated to store and manage chemical libraries in a local or network-accessible MySQL database, and perform various analysis using simple and advanced chemoinformatics methods. Linux and Windows Tool to prepare collection, standalone
LINK SPORES: Structure PrOtonation and REcognition System standalone
LINK KODE solutions istMolBase: dataset management (reading of SMILES and SDF files, depiction, molecule normalization, SMARTS matching), istChemFeat: dataset analysis by means of relevant chemical features research standalone
LINK CLEVER (chemical library editing, visualizing and enumerating resource), tool to manage collection standalone
LINK looking at SMARTS SMARTS chemoinfo, online
LINK OlfactionDB: Odorants are molecules that efficiently carry chemical information, providing one of the main ways for communicating with the environment in all kingdoms of life. In the other hand, mammalian genomes codify for hundreds of olfactory receptors (OR), underlying the crucial role of the sense of smell during evolution, being able to discriminate about 10000 different odors database
LINK LIPIDMAPS provides a range of tools and resources to facilitate lipid research database
LINK French compound collection - CNRS database, need to register
LINK AutoClickChem: performs many click-chemistry reactions in silico. In silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization standalone
LINK iScienceSearch, an Internet search engine for chemists, somewhat a Google for chemistry online, also incorporates PASS (Prediction of Activity Spectra of Substances), Chemicalize (Chemaxon)
LINK ScaffoldTreeGenerator Chemoinformatics - navigation in chemical space, standalone
LINK SeRAPhiC. Data set of 53 high-quality protein-fragment complexes online dataset
LINK BAPPL complexes set. 161 protein-ligand complexes with experimental and estimated binding free energies dataset
LINK Small Molecule Pathway Database (SMPDB) is an interactive, visual database containing more than 350 small molecule pathways found in humans database
LINK SciClips, ddTargets (drug targets / disease target database) database
LINK GDB-11 enumerates small organic molecules up to 11 atoms of C, N, O and F following simple chemical stability and synthetic feasibility rules, other related databases, peptides virtual database
LINK Chemical structure lookup search in search in 74 million indexed structures from over 100 databases (46 million unique structures) database
LINK ClinicalTrials.gov is a registry of federally and privately supported clinical trials conducted in the United States and around the world. ClinicalTrials.gov gives you information about a trial's purpose, who may participate, locations, and phone numbers for more details. This information should be used in conjunction with advice from health care professionals database
LINK Animal drugs database
LINK FDA Animal drugs: Electronic Animal Drug Product Listing Directory online
LINK AMDD: Antimicrobial Drug Database: 2900 antibacterial and 1200 antifungal database
LINK open drug database database
LINK ChemBank: Free collections and utilities, known drugs, many annotated molecules, molecules with druglike and non-druglike properties Compound Database, Compound searching, prescription drugs
LINK PubChemDB is a Java API for working with PubChem data-sets .
LINK PubChem: An information resource linking chemistry and biology Compound Database
LINK Chemical thesaurus : database including chemical entities, interactions, reactions, processes Compound Database
LINK Chemical suppliers and collections Compound Database
LINK Web directory about compound collections and many related links, database search Compound Database, Compound searching
LINK Free collections, about 10000 molecules, if you collaborate with the group Compound Database, part of the French National Compound collection
LINK Free collections Compound Database, online
LINK Crystallography Open Database compounds in 3D, database
LINK NMRShiftDB - Free collection, some molecules are in 3D Compound Database
LINK NMRShiftDB Compound Database
LINK Ligand.Info Utilities such as ligand clustering and ligand similarity search, allows to deal with a file containing compounds Compound searching, clustering, manage database, online
LINK ChemDB: Free collections and utilities such as similarity search, ReactionPredictor... Compound Database, Compound searching
LINK ZINC: Free collections (and links to many commercial vendors), also natural products Compound Databases (about 20), ADME/Tox, Compound searching
LINK The complete DUD-E benchmarking set, the more recent DUD, 2012 datasets
LINK DUD is designed to help test docking algorithms by providing challenging decoys Compounds for different targets, thrombin, FXa...and decoys, datasets
LINK CoCoCo is a free suite of multiconformational molecular databases for High-Throughput Virtual Screening Compound collection in 3D with molecular descriptors, database
LINK ChemMine: Free collections and similarity search utilities, clustering Compound Database, Compound searching
LINK MDLI: Available Chemicals Directory (essentially commercial) Compound Database, Compound searching
LINK Chemnavigator: Commercial collection Compound Database, Compound searching
LINK Dictionary of small molecules. ChEBI: a database and ontology for chemical entities of biological interest Compound Database
LINK DNA DRUG COMPLEX DATA SET Compound Database and Macromolecules
LINK NuBBE database (NuBBEDB) is a virtual database of natural products and derivatives from Brazilian biodiversity Compound Database
LINK BindingDB: Measured binding affinities, macromolecule-ligand complexes Compound Database, Macromolecules
LINK Binding MOAD (Mother of All Databases) Compound Database, Macromolecules
LINK SIDER contains information on marketed medicines and their recorded adverse drug reactions. Profiling profiling, ADMETox, database
LINK STITCH: interaction networks of chemicals and proteins. Profiling Compound Database, Macromolecules, genomes, 2200 drugs, 68000 chemicals
LINK LPDB database: ligand-protein Drug-Ligand Database
LINK MMsINC is a database of non-redundant, richly annotated, and biomedically relevant chemical structures Drug Database
LINK SMILIB : tool to create virtual libraries Virtual Database generator in smiles, standalone
LINK SChiSM2: Create Interactive Web Page Annotations of Molecular Structures Using Jmol Annotate compounds
LINK sMOL Explorer is a 2D ligand-based computational tool that provides three major functionalities: data management, information retrieval and extraction, and statistical analysis and data mining through Web interface. It is an open source, web-enabled database and exploration tool for Small MOLecules datasets, Bioinformatics Data managment - Web interface small molecules
LINK e-LEA3D de novo drug design tool de novo screening scaffold-hopping combinatiorial library design, online
LINK Ilib Diverse: tool to create virtual drug-like libraries Virtual Database generator, standalone
LINK The US National Cancer Institute collections including natural products Compound Database
LINK Main chemical-structures Compound Database, standalone
LINK View properties, purchase compounds Compound Database
LINK View structures and data of Open NCI DB compounds Compound Database
LINK Find compound properties Compound searching
LINK Similarity search and other tools Compound searching
LINK Chemspider Compound searching and several utitilities
LINK Chembl, database of bioactive molecules Compound search, Annotated database
LINK Chemistry Databases on the Web Chemistry Databases, online
LINK The web of chemical informatics Chemistry blog
LINK Find chemicals in the ChemExper Chemical Directory online database
LINK With eMolecules you can draw your chemical structure and instantly search millions of molecules from across the Web and from chemical suppliers worldwide Compound searching online
LINK PDBeChem : Consistent and enriched library of ligands, small molecules and monomers that are referred as residues and hetgroups in any PDB entry Compound Database from the PDB, Compound searching, X-ray, online
LINK Ligand-Expo (formerly Ligand Depot) provides chemical and structural information about small molecules within the structure entries of the Protein Data Bank online
LINK PDB-Ligand online
LINK SuperLigands a database of ligand structures derived from the Protein Data Bank with similarity searches and other tools online
LINK Chemistry and biology database: numerous links (databases, tools) valuable for drug design projects Compound Database, macromolecules links to programs
LINK HIC-Up Hetero-compound Information: Small molecules from the PDB Compound Database from the PDB, online
LINK The directory of chemistry on the WWW since 1993 Numerous chemistry links
LINK Compound collection and building blocks Compound Database online
LINK QueryChem : searches public databases using text and structure Compound Database, Compound searching, online
LINK The Prestwick Chemical Library is a unique collection of about 1120 high-purity chemical compounds (all off patent) carefully selected Off patent compound collections for experimental testing
LINK The Spectrum Collection 2000 biologically active and structurally diverse compounds from our libraries of known drugs, experimental bioactives, and pure natural products. SDF file available Structurally diverse compounds for experimental screening and in silico work
LINK SeqChem is an internet based company, specialising in biochemicals and other natural products. They provide a simple and cost effective way to fullfil chemical needs Compounds for experimental screening
LINK DTP maintains a repository of synthetic and natural products that have been evaluated as potential anticancer and anti-HIV agents. This repository has an historic inventory of more than 140,000 non-discreet compounds that have been submitted to DTP from a variety of sources worldwide. Compound collections for experimental or in silico screening
LINK Marvel Library - A Collection of Over 9000 Unique Compounds .
LINK TCMGeneDIT is a database system providing association information about traditional Chinese medicines (TCMs), genes, diseases, TCM effects and TCM ingredients automatically mined from vast amount of biomedical literature Database online, natural products
LINK TCM Database Taiwan: Largest Traditional Chinese Medicine Database for Drug Screening In Silico Ligand Database online
LINK TCMID: Traditional Chinese Medicine integrative database for herb molecular mechanism analysis Ligand Database online
LINK Indian Plant Anticancer Compounds Database (Ayurvedic medicine) Database online (the site is moving and may not work from time to time)
LINK Database on pharmacophore analysis of active principles, from medicinal plants database


URLs 3D structure generator Comments
LINK Tautomer generator is a program that generates a set of molecules (tautomers) from a molecular core and number of hydrogen atoms Simulation tools, standalone
LINK NEWLEAD is a computer program for the automatic generation of candidate structures Compound searching - newlead, standalone
LINK LSD for automatic structure elucidation of small organic molecules from 2D NMR data standalone
LINK Corina: 2D to 3D conversion commercial demo
LINK Omega: 2D to 3D conversion commercial demo
LINK ICM: 2D to 3D conversion commercial demo
LINK XDrawChem: Possible 2D to 3D conversion with BUILD3D .
LINK stereoisomer generation online for one compound with Molgen online
LINK The pre-compiled version of Cyndi (Windows), parameter input file, Tripos force field parameter file and the test set of 329 high-resolution and drug-concerned small molecules determined from X-ray structures in mol2 format standalone
LINK Smiles to 3D SDf and then structural optimization of the 3D structure mmff standalone
LINK PRODRG2 Server online
LINK 2D to 3D with Corina online
LINK EasyMol: A Java tool standalone
LINK VeraChem online
LINK Balloon 2d to 3d structure generator standalone
LINK VEGA ZZ can be found online
LINK MolEdit Web server for 2D molecular editor & 3D structure optimization online
LINK Crystallography Open Database compounds in 3D, database
LINK NMRShiftDB - Free collection, some molecules are in 3D Compound Database
LINK FROG2 online
LINK DG-AMMOS online and standalone, see also AMMOS to minimize molecules once docked into a binding site
LINK ChemoPy: freely available python package for computational biology and chemoinformatics standalone (linux, windows)
LINK WEBCDK: 2d to 3d, for now it does not seem to work, should be somewhere here http://crdd.osdd.net/, no comments after email contact online
LINK MolEdit online
LINK Probuilder: Peptide builder online
LINK smi23d online


URLs Homology modeling & 3D Quality control Comments
LINK The Dali server is a network service for comparing protein structures in 3D online, structural analysis, compare structures
LINK EMBOSS is The European Molecular Biology Open Software Suite. Popular applications include: prophet Gapped alignment for profiles; infoseq Displays some simple information about sequences; water Smith-Waterman local alignment; pepstats Protein statistics; showfeat Show features of a sequence; palindrome Looks for inverted repeats in a nucleotide sequence; eprimer3 Picks PCR primers and hybridization oligos; profit Scan a sequence or database with a matrix or profile; extractseq Extract regions from a sequence; marscan Finds MAR/SAR sites in nucleic sequences; tfscan Scans DNA sequences for transcription factors; patmatmotifs Compares a protein sequence to the PROSITE motif database; showdb Displays information on the currently available databases; wossname Finds programs by keywords in their one-line documentation; abiview Reads ABI file and display the trace; tranalign Align nucleic coding regions given the aligned proteins online and standalone
LINK The Fold and Function Assignment System (FFAS) server online, structural analysis
LINK CD-HIT is a widely used program for clustering and comparing protein or nucleotide sequences (see also the standalone version) online, sequence clustering
LINK Supercharge refers to increasing the net charge of a protein by mutating surface residues. Increasing net charge can improve reversibility of unfolding by preventing aggregation of partially unfolded states online, avoid protein aggregation
LINK SwissSidechain: a molecular and structural database of non-natural aa sidechains (for peptides and proteins) database
LINK foXs: Fast SAXS Profile Computation with Debye Formula online
LINK GeneSilico Metaserver: This is a gateway to various methods for protein structure prediction online
LINK PINALOG: a novel approach to align protein interaction networks, implications for complex detection and function prediction online
LINK CombFunc: predicting protein function using heterogeneous data sources. The CombFunc web server, which makes Gene Ontology (GO)-based protein function predictions online
LINK Protinfo ABCM: protein structure prediction online
LINK HH-suite sequence alignments: ftp://toolkit.genzentrum.lmu.de/pub/HH-suite/ standalone
LINK HH-suite sequence alignments, with the other tools online
LINK HHfrag: HMM-based fragment detection using HHpred online
LINK SAFrag 1.0 Efficient candidate fragment search from amino acid sequence online
LINK PIGS Server (Prediction of Immuno Globulin Structure) online, nice logo with the head of 3 cute little pigs surrounding an Ab
LINK pKNOT v.2: the protein KNOT web server online
LINK COFACTOR: an accurate comparative algorithm for structure-based protein function annotation online
LINK HHpred - Homology detection & structure prediction by HMM-HMM comparison online
LINK PSiFR (Protein Structure and Function predicton Resource) online
LINK EsyPred3D homology modeling (you can easily select your template) online
LINK GPCR-ITASSER homology modeling for GPCR online
LINK GPCR modeling and simulation toolkit online
LINK GPCR-SSFE homology modeling for GPCR online
LINK WAM antibody online
LINK RosettaAntibody online
LINK Make sequence file from PDB file online
LINK CBS Prediction Servers: numerous tools to analyze protein sequences, Post-translational modifications of proteins, Protein function and structure: ChloroP LipoP NetNES SecretomeP SignalP, TargetP TatP DictyOGlyc NetAcet NetCGlyc NetCorona NetGlycate NetNGlyc NetOGlyc NetPhorest NetPhos NetPhosBac NetPhosK NetPhosYeast NetPicoRNA NetworKIN, ProP, YinOYang , distanceP, EPipe (Functional differences of protein variants), InterMap3D, NetSurfP, NetTurnP , ProtFun, RedHom (Reduction of sequence similarity in a data set), TMHMM, VarDom Glycosylation and many other tools online
LINK The NetOglyc server produces neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins Glycosylation, online
LINK GlycoPP is a webserver for predicting potential N-and O-glycosites in prokaryotic protein sequence(s) Structural bioinformatics Glycosylation, online
LINK GlyProt performs an in silico glycosylation of proteins. The 3D structure of protein is required as input. Potential N-glysylations site are automatically detected. The attached glycan are constructed with SWEET-II Structural bioinformatics Glycosylation, online
LINK The Uppsala Electron Density Server: check your favorite experimental Xray structure Protein X-ray structural analysis
LINK SeqAlert(c) is a sequence alerting service that will periodically compare your sequence(s) against sequences from determined 3D structures, or structures being determined ... Information about the 3d structure you are waiting for
LINK WoLF PSORT: Protein Subcellular Localization Prediction Protein Subcellular Localization Prediction online
LINK FoldIndex tries to answer to the question: Will this protein fold? Structural Analysis, folding online
LINK The RECON server predicts residue contacts using correlated mutation method with set of filters to reduce the false positives Analysis of the quality of the 3D structure online
LINK The PROFcon server uses neural network method that utilizes sequence information, secondary structure and solvent accessibility predictions, and the overall properties of the entire protein to predict residue contacts standalone
LINK The CORNET server is a neural network based predictor that uses as input correlated mutations, sequence conservation, predicted secondary structure and evolutionary information Analysis of the quality of the 3D structure online
LINK Atlas of Side-Chain and Main-Chain Hydrogen Bonding, it gives values Structural analysis, Protein Structure, course
LINK GANGSTA+ is a non-sequential structure-alignment tool, compare the structure of a protein with more than 10,000 others. Compare the structures of a pair of proteins and perform a sequence scoring Structural bioinformatics oline
LINK Biskit is a modular, object-oriented Python library for structural bioinformatics research Python library for structural bioinformatics research, standalone
LINK Swissmodel: homology modeling online
LINK Robetta: homology modeling online
LINK I-TASSER: homology modeling online
LINK QUARK Internet service for ab initio protein folding and protein structure prediction online
LINK IntFOLD: Integrated Protein Structure and Function Prediction Server online
LINK GPCRautomodel: homology modeling online
LINK Geno3D: AUTOMATIC MODELING OF PROTEINS THREE-DIMENSIONAL STRUCTURE online
LINK LOMETS: (Local Meta-Threading-Server) web service for protein structure prediction online
LINK 3djigsaw: This server builds three-dimensional models for proteins based on homologues of known structure online
LINK BSR Binding Site Refinement employs a new template-based method for the local refinement of ligand-binding regions in protein models using closely as well as distantly related templates identified by threading online
LINK Memoir: template-based structure prediction for membrane proteins online
LINK Links to Macromolecular structures in 3D Databases of Macromolecules in 3D, online
LINK The Protein Data Bank 3D structure database online
LINK The Entrez Structure Database Macromolecule database online
LINK PDBCat can be used to manipulate and process PDB files using commonly available tools such as Perl, awk, etc. Tools to manipulate PDB files, standalone
LINK Atlas of protein side-chain interactions within known protein structures and interactions with DNA Macromolecule interaction database, online
LINK Glycoconjugate Data Bank:Structures and annotated glycan structure database and N-glycan primary structure verification service online
LINK Many structural bioinformatics tools Tools to analyze macromolecules online
LINK Many tools for structural bioinformatics, loop prediction, simulation, structural refinement of proteins with Gromacs, Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent, small molecules Structural bioinformatics online
LINK The UCLA-DOE Structure Evaluation server is a tool designed to help in the refinement of crystallographic structures and models Validate protein structure online
LINK ERRAT is a protein structure verification algorithm Validate protein structure online
LINK UCLA-DOE many links and online tools for protein structure prediction and analysis online
LINK SCWRL 4 is the most recent version of the SCWRL program for prediction of protein side-chain conformations Predict protein side chain conformation
LINK SCit is a web server providing services for protein side chain conformation analysis and side chain positioning online
LINK Bodil : biomolecular modeling package Molecular modeling standalone
LINK GalaxyWEB server for protein structure prediction and refinement online
LINK DOMpro is a web server to predict protein domain boundaries online, domain prediction
LINK CDD server: Search for Conserved Domains within a protein sequence online, domain prediction
LINK pDomain resource is centered around defining structural domains from 3D coordinates online, domaine prediction
LINK MaxSprout is a fast database algorithm for generating protein backbone and side chain co-ordinates from a C(alpha) trace online
LINK Seq2Struct, a web resource for the identification of sequence-structure links online
LINK Modeller: software package for homology or comparative modeling of protein 3D structures Homology modeling, standalone
LINK Jackal: protein structure modeling package Homology modeling, loop prediction related tools, standalone
LINK PSIPRED web servers performing secondary structure prediction, transmembrane topology prediction or protein fold recognition Protein structure prediction online
LINK BinMemPredict: a web server and software for predicting membrane protein types Protein membrane online
LINK OPM database and PPM web server: resources for positioning of proteins in membranes Protein membrane online
LINK PredictProtein: webserver for homology modeling and protein function prediction Homology modeling related tools online
LINK Prospect-PSPP: automatic computational pipeline for protein structure prediction Protein structure prediction online
LINK Robetta: web server for protein structure prediction and analysis Protein structure prediction online
LINK SPACE server includes tools for predicting and analyzing structures of biomolecules and their complexes online
LINK CAMPO, SCR_FIND, CHC_FIND : web tools to analyze evolutionary conserved residues, structurally conserved regions and conserved hydrophobic contacts Protein structure analysis online
LINK CHC_FIND: Conserved Hydrophobic Contacts (CHCs) are defined as residue-residue hydrophobic contacts involving only apolar atoms online
LINK CAMPO: is a tool useful for the identification of conserved amino-acid sites among sequence homologues online
LINK Pred-TMBB: web server for predicting the topology of beta-barrel outer membrane proteins Protein structure prediction online
LINK ProteinDBS: web server for detection of similar protein tertiary structures Protein structure analysis, Structural similarity search, online
LINK FATCAT: web server for flexible structure comparison and structure similarity searching Protein structure analysis, Structural similarity search online
LINK CaspR : web server for automated molecular replacement, method of choice for X-ray crystallography structure determination when structural homologues are available in PDB, using homology modeling Protein structure determination online
LINK PREDITOR: Program for predicting dihedral angles from chemical shifts and/or sequential homology Protein structure determination online
LINK SABBAC: online structural alphabet-based protein backbone reconstruction from alpha-carbon trace Protein structure prediction
LINK PS2: protein structure prediction server: automated homology modeling server using a consensus strategy between psi-blast, impala and T-coffee with a final 3D structure modeled with Modeller Homology modeling, related tools online
LINK TransFold : web server for predicting the structure and residue contacts of transmembrane beta-barrels Protein structure prediction online
LINK Harmony: web server for the assessment of protein structures Protein structure validation online
LINK RosettaDesign: Server for identifying low energy amino acid sequences from the backbone coordinates of the target structure Protein structure prediction onine
LINK MolProbity: web server for structure validation and all-atoms contact analysis for nucleic acids and their complexes Protein structure validation online
LINK Decoys R: database of computer generated conformations of proteins sequences that possess some characteristics of native proteins Protein structure validation online
LINK iSee: iSee is an intuitive and interactive approach for the dissemination of structural biology data Protein structure analysis, annotation, standalone
LINK Automatic threading, optimization modeling and evaluation, homology modeling (Douguet and Labesse) Protein structure prediction online
LINK TarO analyses a protein sequence by a large number of bioinformatics techniques online
LINK The Jpred 3 secondary structure prediction server. A Secondary Structure Prediction Server Protein structure prediction online
LINK ModBase: Database of Comparative Protein Structure Models database of homology models
LINK ESPript, Easy Sequencing in Postscript, is a utility to generate a pretty PostScript output from aligned sequences Protein structure prediction, sequences, standalone
LINK RaptorX is a new protein structure prediction program online, got very good results at CASP9 for instance
LINK CPHmodels 3.2 Server homology modeling server at DTU online
LINK ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage. This novel method makes it possible to accurately dock atomic structures into low-resolution electron-density maps Docking modules into low resolution electron-density maps, can help for homology modeling of large structures


URLs PPI docking, databases, hot spots Comments
LINK PIE (Protein Interaction information Extraction) information about protein-protein interaction - PPI
LINK Protein-Protein Docking with F(2)Dock 2.0 and GB-Rerank PPI docking, online site 1
LINK Protein-Protein Docking with F(2)Dock 2.0 and GB-Rerank PPI docking, online site 2
LINK Protein-protein binding affinity prediction on a diverse set of structures .
LINK PPI Prediction Server classifies a protein-protein complex concerning its interaction type into permanent, transient or crystal artifact. The discrimination is performed using two characteristics of the protein-protein complex, the hydrophobicity of the interface and the quotient of interface area ratios online
LINK PTools : a C++ and Python library for macromolecular docking standalone
LINK ATTRACT-Docking Program (Fortran-Version, full source code and manual) standalone
LINK BLASTCLUST automatically and systematically clusters protein or DNA sequences based on pairwise matches found using the BLAST algorithm in case of proteins or Mega BLAST algorithm for DNA, remove redundant sequence information standalone
LINK Proface: Analysis of protein-protein interface online online
LINK PI2PE : protein interface-interior prediction engine online
LINK 3D-Surfer offers web-based tools for rapid protein surface analysis and comparison. The server integrates various methods to assist in the high throughput screening and visualization of protein surface comparisons online
LINK InterProSurf: Protein-Protein Interaction Server online online
LINK Investigating MacroMolecular Interfaces with Intervor online
LINK PDBePISA (Protein Interfaces, Surfaces and Assemblies) online
LINK SwarmDock: a server for flexible protein-protein docking online docking
LINK PRUNE and PROBE--two modular web services for protein-protein docking docking online
LINK The TissueNet database of human tissue protein-protein interactions database online
LINK BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference online
LINK PrePPI: a structure-informed database of protein-protein interactions database
LINK Global and Restrained Docking Exploration Nexus 3D-GARDEN is a state-of-the-art comprehensive software suite and server for protein-protein docking with full high-performance computing functionality online docking
LINK I2I-SiteEngine Structural and Physico-Chemical Alignment of Protein-Protein Interfaces online
LINK BIND: The Biomolecular Interaction Network Database Macromolecule interaction database
LINK DIP: Database of interacting proteins Macromolecule interaction database, PPI
LINK CORUM: the comprehensive resource of mammalian protein complexes Macromolecule interaction database
LINK DOMINE: a database of protein domain interactions Macromolecule interaction database
LINK PepCyber:PPEP: a database of human protein-protein interactions mediated by phosphoprotein-binding domains Macromolecule interaction database
LINK HIPPIE Human Integrated Protein-Protein Interaction rEference Macromolecule interaction database
LINK The Biological General Repository for Interaction Datasets (BioGRID) database Macromolecule interaction database
LINK Druggable Protein-protein Interaction Assessment System Dr PIAS Protein-protein interaction PPI
LINK Numerous information and links: protein interaction network and databases of complexes can be found at the JCB Protein-Protein Interaction Website links and tools for macromolecular interactions
LINK PSIbase : a database of Protein Structural Interactome map (PSIMAP) Protein interaction database
LINK Structural Interactome Map of all Proteins PSIbase is a molecular interaction database
LINK SCOPPI: a structural classification of protein-protein interfaces Protein-protein database
LINK the DOCKGROUND resource implements a comprehensive database of co-crystallized (bound-bound) protein-protein complexes Database of experimental complexes
LINK The FireDock server addresses the refinement problem of protein-protein docking solutions Macromolecular docking online
LINK Grammx: Tools for protein-protein docking. GrammX: web interface of Gramm Macromolecular docking online, see also standalone
LINK GWIDD : genome wide docking database, GWIDD is an integrated resource for structural studies of protein-protein interactions on genome-wide scale online
LINK MolSurfer a macromolecular interface navigator Interface analysis standalone and online
LINK LIGIN: Molecular docking using surface complementarity. The LIGIN program is also available as part of the WHATIF software package Macromolecular docking standalone
LINK Protein docking tools (PatchDock) and related. PatchDock, webserver for macromolecules and small molecules docking based on shape complementarity criteria. There are many other tools here including tools for peptides, flexibility, comparing binding pockets... online docking
LINK Biomolecular modelling group: several tools for PPIs online and standalone
LINK AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models online
LINK DOCK/PIE(RR): Protein Docking Server Macromolecular docking online
LINK STRING is a database of known and predicted PPI database
LINK The PINA protein interaction database and Interactome files database
LINK HPRD, Human Protein Reference Database, it represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome database
LINK Drug-SNPing: an integrated drug-based, protein interaction-based tagSNP-based pharmacogenomics platform for SNP genotyping All drug-based and protein-protein interaction-based SNP genotyping information are provided with PCR-RFLP (PCR-restriction enzyme length polymorphism) and TaqMan probes online
LINK Interactome3D is a web service for the structural annotation of protein-protein interaction networks online
LINK MINT, the Molecular INTeraction database online database
LINK iRefWeb is a web interface to a broad landscape of data on protein-protein interactions (PPI) online search for PPI related data
LINK Intact: open source database system and analysis tools for molecular interaction data. As from September 2011, IntAct contains approximately 275000 curated binary interaction evidences from over 5000 publications online database
LINK The IMEx consortium is an international collaboration between a group of major public interaction data providers who have agreed to share curation effort online database
LINK PS-HomPPI is a sequence-based partner-specific protein-protein interface residue prediction server online
LINK NPS-HomPPI is a sequence-based non-partner-specific protein-protein interface residue prediction server online
LINK PBSword is a web server designed for efficient and accurate comparisons and searches of geometrically similar protein-protein binding sites from a large-scale database online
LINK SynSysNet, which is based on an expert-curated list of 1.000 human genes, specific to the synapse. Information on resulting proteins, their 3D structure, binding small molecules Protein-Protein-Interactions (PPIs) and Compound-Protein-Interactions are integrated online
LINK DOMINO is an open-access database comprising more than 3900 annotated experiments describing interactions mediated by protein-interaction domains online database
LINK SNAPPI stands for Structures, iNterfaces and Alignments for Protein-Protein Interactions SNAPPI-DB is an object-oriented database of domain-domain interactions SNAPPI-Predict is a protein-protein interaction prediction program which is currently in development SNAPPI-View is the web interface to SNAPPI-DB and SNAPPI-Predict online
LINK InterEvScore: A novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution standalone
LINK KBDOCK is a 3D database system that defines and spatially clusters protein binding sites for knowledge-based protein docking. KBDOCK integrates protein domain-domain interaction information from 3DID and sequence alignments from PFAM together with structural information from the PDB in order to analyse the spatial arrangements of DDIs by Pfam family, and to propose structural templates for protein docking Database PPI
LINK pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring online
LINK PyDock: tool for protein-protein docking Macromolecular docking online
LINK Trypano-PPI: a web server for prediction of unique targets in trypanosome proteome online
LINK Presaging Critical Residues in Protein interfaces-Web server implements a recently described and highly accurate computational tool designed to predict critical residues in protein interfaces: PCRPi online
LINK CPORT is an algorithm for the prediction of protein-protein interface residues online
LINK Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function database online
LINK SKEMPI, a database of 3047 binding free energy changes upon mutation assembled from the scientific literature, for protein-protein heterodimeric complexes with experimentally determined structures database to download
LINK HADDOCK: docking driven by interface restraints Macromolecular docking, also online
LINK SmoothDock Macromolecular docking online
LINK iMolTalk: On-line tools including detection of the interface between two chains of a structure Interface analysis online
LINK Bipdock: Bielefeld Protein Docking Software Macromolecular docking standalone
LINK ZDOCK: docking based on FFT search Macromolecular docking, standalone
LINK ClusPro: protein-protein docking webserver using 3 docking programs - DOT ZDOCK GRAMM Macromolecular docking online
LINK Protein Interactions Calculator (PIC) Protein-protein energy computation, online, structural analysis
LINK DOT: protein-protein docking software Macromolecular docking standalone
LINK ROSIE, including rosetta Protein-protein docking Macromolecular docking online
LINK DrugscorePPI is a knowledge-based scoring function for computational alanine-scanning in protein-protein interfaces Hot-Spots online
LINK ANCHOR is a web-based tool whose aim is to facilitate the analysis of protein-protein interfaces with regard to its suitability for small molecule drug design Hot-Spots online
LINK KFC Server: interactive forecasting of protein interaction hot spots Hot-Spots online
LINK HotSprint: database of computational hot spots in protein interfaces Hot-Spots
LINK CombDock: combinatorial assembly of multiprotein complexes by multiple docking (see also Firedock) Macromolecular docking standalone
LINK The RosettaDock server Macromolecular docking
LINK BDOCK: protein-protein docking software integrating the degree of burial of surface residues into protein-protein docking Macromolecular docking standalone
LINK MolFit : protein-protein docking software estimating the extent of geometric and chemical surface complementarity Macromolecular docking
LINK Hex protein-protein docking and molecular superposition program Macromolecular docking online
LINK ESCHER-NG: protein-protein and DNA-protein docking software Macromolecular docking
LINK FTDock (Fourier Transform Dock) Macromolecular docking standalone
LINK Prism Protocol Binding site analysis, prediction, standalone
LINK FastContact: a free energy scoring tool for protein protein complex structures (PPI) Macromolecular scoring (PPI) online
LINK PIER: prediction of interfaces based on atomic statistical propensities online
LINK scoring function named as SPA-PP, specificity and affinity of the protein-protein interactions (algorithm is implemented in C language Bioinformatics, 2013 29:1127-33) standalone
LINK meta-PPISP: meta server for interface prediction using cons- PPISP, PINUP and Promate online
LINK pyDockNIP: prediction of binding hot-spots from docking online
LINK FTMap: Computational solvent mapping is a powerful tool to understand interactions between proteins and solvent molecules. It docks small organic molecules on a protein surface, finds favorable binding positions, clusters the conformations of all prediction, and ranks the clusters on the basis of their average free energy. The low energy clusters are grouped into consensus sites and the largest consensus sites are able to identify actice or ligand binding sites. The docked fragments can also be served as the building blocks for fragment-based drug design online
LINK FOLDEF: energy-based alaninescanning of a protein complex structure online
LINK HotPoint: prediction of binding hot-spots based on accessibility and knowledge-based potentials hot spot
LINK ISIS: sequence-based neural network method for prediciton of binding hot-spot residues .
LINK ProMate: prediction of potential protein-protein binding sites Binding site prediction online
LINK WHISCY: interface prediction based on conservation and surface properties online
LINK ODA (Optimal Docking Areas) Binding site prediction online
LINK SPIN-PP is a database of all protein-protein interfaces present in the PDB Macromolecule interaction database
LINK PPI databases, tools many links .
LINK PLATINUM is designed for calculation of hydrophobic properties of molecules and their match or mismatch in receptor–ligand complexes. These properties may help to analyze results of molecular docking .
LINK Analysis of interatomic Contacts in Ligand-Protein complexes
Analysis of interatomic contacts in protein entries		 Analysis of interatomic Contacts
LINK SCOWLP is a web-based relational database formed by eleven tables describing PDB interface interactions at atom Interfaces - databases online
LINK the ADP_EM method makes it possible to accurately dock atomic structures into low-resolution electron-density maps Docking in electron-density maps derived from for instance electron microscopy standalone
LINK See also The Fast Atomic Density Evaluator (FADE) and Pairwise Atomic Density Reverse Engineering (PADRE). Many tools Predict binding sites and analyze docked complexes
LINK 3D-partner: a web server to infer interacting partners and binding models online
LINK Protein segment finder: an online search engine for segment motifs in the PDB online
LINK 3did A collection of domain-domain interaction structures and catalogue of domain-peptide structural motifs in the PDB online
LINK HotSpot Wizard: a web server for identification of hot spots in protein engineering online
LINK siteFiNDER 3D: a web-based tool for predicting the location of functional sites in proteins online
LINK Firestar prediction of functionally important residues online
LINK The TissueNet database of human tissue protein-protein interactions Protein-protein analysis (PPI), online
LINK XLink-DB: Database and Software Tools for Storing and Visualizing Protein Interaction Topology Data online and the source code can also be found at sourceforge.net
LINK PrePPI: a structure-informed database of protein-protein interactions, over 370 000 PPIs for human are considered high confidence Protein-protein analysis (PPI)
LINK The 2P2I Database, list of complexes and druggability prediction of the interface online
LINK PPI-HitProfiler: In silico filter to build a compound collection enriched in PPI inhibitors (CDithem) Protein-protein inhibitors (PPI), standalone python
LINK iPPI-DB contains 1600 non-peptidic inhibitors (iPPI) accross 12 classes of protein-protein interactions (PPI). The chemical structures of iPPI are manually extracted from the literature (peer-reviewed articles or world patents) along with their phamacological profile and store in iPPI-DB (CDithem project) PPI online curated database
LINK Atomic Interactions and Profile of Small Molecules Disrupting PPI Interfaces: the TIMBAL Database PPI online database
LINK AnchorQuery is a specialized pharmacophore search technology that brings interactive virtual screening of novel protein-protein inhibitors to the desktop Protein-protein inhibitors online
LINK ProMateus: an open research approach to protein-binding sites analysis Mutation and docking/binding online
LINK HyPare is a newly designed tool based on the PARE algorithm (Predicting Association Rate Enhancement). With HyPare you can find hotspots for association, and thus, engineer molecules... Mutation and docking/binding online
LINK OCA, a browser-database for protein structure/function Structural Analysis, online
LINK The program PARE calculates the change in rate of association (kon) of mutant protein-protein interaction complexes from the change in the Debye Huckel energy of interaction Structural Analysis, binding, mutations, online


URLs Simulation, Electrostatics Comments
LINK Wolf2Pack : Portal Based Atomistic ForceField Development standalone and online
LINK Smina: A fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization standalone
LINK ALADYN dynamics-based alignment of proteins (The ALADYN web server aligns pairs of protein structures by comparing their internal dynamics and detecting regions that sustain similar large-scale movements. The latter often accompany functional conformational changes in proteins and enzymes. The ALADYN dynamics-based alignment can therefore highlight functionally-oriented correspondences that could be more elusive to sequence or structure-based comparisons) online
LINK Radius of Gyration online
LINK The Ligand Binder helps the user generate a series of CHARMM inputs to calculate a protein/ligand binding free energy (CHARMM-GUI) Online tools for Charmm
LINK ParamChem will contribute to develop an integrated cyber environment to address the simulation needs of molecular sciences. The proposed infrastructure will provide reference data organizers and generators as well as workflows for automatic parameterization of Molecular Mechanics (MM) Force Fields as well as Semi-Empirical (SE) methods Online tools, links to Charmm, you need registration
LINK iBIOMES Disseminating simulation data to create knowledge Simulation, online, you need registration
LINK Web interface for Brownian dynamics simulation of ion transport and its applications to beta-barrel pores Simulation, Charmm, Online
LINK The NMSim web server implements a three-step approach for multiscale modeling of protein conformational changes Simulation online
LINK Monte Carlo tool Simulation tools
LINK Many tools for structural bioinformatics, loop prediction, simulation, structural refinement of proteins with Gromacs, Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent, small molecules Structural bioinformatics online
LINK The CAMD Open Software project (CAMPOS) is a collection of programs for atomic-scale simulations Simulation tools
LINK Local move is a Monte-Carlo approach to the problem of finding best-fitting lattice models for biopolymers. Simulation tools - Flexibility - Structure Prediction Analysis
LINK PredyFlexy: flexibility and local structure prediction from sequence .
LINK KoBaMIN: a knowledge-based minimization web server for protein structure refinement .
LINK Dynameomics is a continuing project to characterize the native state dynamics and the folding / unfolding pathway of representatives from all known protein folds by molecular dynamics simulation Simulation
LINK iFold: a web portal for interactive protein folding/unfolding simulations... performs discrete molecular dynamics simulations of proteins using coarse-grained structural models Simulation
LINK MD-TRACKS is a collection of command line tools and a python package to facilitate and automate the analysis of molecular dynamics and monte carlo simulations Simulation
LINK clickMD molecular dynamics in one click (Andrea Cristiani et al) online molecular dynamics
LINK gromacs .
LINK (Pro)tein (B)ilayer (L)ipid (M)embrane (ProBLM) is a webserver and stand-alone desktop application that creates a combined protein-membrane complex when given a membrane protein (helical or beta-barrel) and bilayer lipid membrane (POPC or POPE) online and standalone
LINK Lipid membrane in 3D .
LINK Tinker .
LINK Towhee is a Monte Carlo molecular simulation .
LINK AMMP is a modern full-featured molecular mechanics, dynamics and modeling program .
LINK PINY_MD is capable of performing a wide variety of molecular dynamics .
LINK WEBnm@: a web application for normal mode analysis of proteins .
LINK PBEQ-Solver for online visualization of electrostatic potential of biomolecules Electrostatics
LINK pKa calculations with the FD/DH method (Warwicker Group) Electrostatics, standalone
LINK This PIPSA service is provided for the comparison of the electrostatic interaction properties of proteins Electrostatics
LINK Online tools to compute protein electrostatics based on MEAD (Bashford and Karplus 1990): PCE (Protein Continuum Electrostatics). See PCE pKa and electrostatics Electrostatics, online
LINK H++, pKa Electrostatics, online
LINK Bluues server: electrostatic properties of wild-type and mutated protein structures Electrostatics, online
LINK Web servers and services for electrostatics calculations with APBS and PDB2PQR Electrostatics, online
LINK DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol Electrostatics, online
LINK POLYVIEW-MM. Web-based platform for animation and analysis of molecular simulations online
LINK CLICK. Web server for superimposing the 3D structures of any pair of biomolecules .
LINK A web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating across membrane transporters .
LINK R.E.D. Server. Web service designed to automatically derive RESP and ESP charges .
LINK Program ChemSol is designed for the calculations of solvation free energies using the Langevin Dipoles (LD) solvation model .
LINK SuperPose is a protein superposition server .
LINK ProPka Electrostatics
LINK APBS (Baker et al. 2001): software package for the numerical solution of the Poisson-Boltzmann equation Electrostatics
LINK Open Protein Simulator (OOPS) Molecular simulations
LINK WhatIf: web interface to the versatile molecular modeling package online, modeling structural analysis
LINK Constraint Network Analysis (CNA): A Python Software Package for Efficiently Linking Biomacromolecular Structure, Flexibility, (Thermo-)Stability, and Function Molecular simulations, standalone
LINK elNemo is the Web-interface to The Elastic Network Model (Gohlke group, paper by Pfleger et al 2013) Molecular simulations, online
LINK Non covalent bond finder Structural analysis
LINK MODEL - Molecular Descriptor Lab for Computing structural and physichemical properties of molecules from their 3D structures Molecular Descriptor from 3D
LINK SVMProt: protein functional family prediction Structural analysis
LINK SODIUM - Arrange ions around biological macromolecules .
LINK GULP is a program for performing a variety of types of simulation Molecular simulations
LINK The Biomolecule Toolkit Molecular modeling
LINK YUP: A Molecular Simulation Program for Coarse-Grained and Multiscaled Models (Python) Molecular simulations
LINK oGNM (Yang et al. 2006): calculating the equilibrium dynamics of any structure submitted in PDB format, using the Gaussian network Model (GNM) Molecular simulations, flexibility
LINK ProtoMol: object-oriented component based framework for molecular dynamics simulations Molecular simulations
LINK PDB_Hydro Tools for mutating and solvating protein structures .
LINK NOMAD-Ref (Lindahl et al. 2006): Tools using normal modes for structural refinement of large proteins Molecular simulations
LINK FSolv: fast method for the determination of fractional contributions to solvation in proteins Solvation
LINK ILM (Ruan et al. 2004): web server combining two algorithms, iterated loop matching and maximum weighted matching, for predicting RNA secondary structures RNA structure prediction
LINK RDfolder (Ying et al. 2004): webserver for prediction of RNA secondary structure from two methods, random stacking of helical regions and helical regions distribution RNA structure prediction
LINK NAMD: molecular dynamics package for simulation of large biomolecular systems Molecular simulations
LINK CHARMM (Chemistry at HARvard Molecular Mechanics) is a program for macromolecular simulations Molecular simulations
LINK many perl scripts to analyze a protein, add ions, compute volume, add ions in a box of water, tools for Python, compute energy.. Analyze protein structures
LINK Scripts for manipulating molecules scripts to help prepare organic molecules for simulation
LINK AmberTools12 Analyze protein structures
LINK Python macromolecular library..many tools to study PDB files, geometry, viewer... mmLib, Class for least-squares structural superposition... Analyze protein structures
LINK Many tools for proteins, statistics about your PDB file, volume... Uppsala Software Factory Analyze protein structures
LINK RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes Analyze protein structures - RMSD
LINK superimpose 3D structural superposition server .
LINK PDB2PQR Server .
LINK PRODRG will take a description of a small molecule (as PDB coordinates / MDL Molfile / SYBYL Mol2 file / text drawing) and from it generate a variety of topologies for use with GROMACS, WHAT IF, Autodock, HEX, CNS, REFMAC5, SHELX, O and other programs, as well as energy-minimized coordinates in a variety of formats .
LINK This service provides topology and parameters for small organic molecules compatible with the CHARMM all atoms force field, for use with CHARMM and GROMACS .
LINK B is a Java-based, on-line biomolecular modeling package Molecular modeling
LINK GROMACS (Van Der Spoel et al. 2005) is a package for performing standard MD simulations, energy minimizations, NMR refinement Molecular simulations
LINK Molecular Dynamics Extended Library (Database of Molecular Dynamics Trajectories) Molecular simulation database
LINK The Uppsala Electron Density Server (Kleywegt et al. 2004) Protein X-ray structural analysis
LINK BioShell is a suite of programs designed for pre- and post-processing in protein structure modeling protocols Tools to prepare molecules for simulations
LINK Protein Dipole Moments Server: Electrostatics: dipole moment
LINK PAT: a protein analysis toolkit for integrated biocomputing on the web Structural Analysis
LINK Patch Finder Plus (PFplus): A web server for extracting and displaying positive electrostatic patches on protein surfaces .
LINK The MORPH server produces 2D and 3D animations of a plausible or semi-plausible pathway between two submitted protein subunit conformations. See also database of macromolecular movements. Receptor flexibility Structural analysis
LINK DFprot server provides deformability/flexibily analysis of your 3D structure Macromolecule Flexibility online
LINK AD-ENM server provides a spectrum of analyses for the dynamics of an elastic network model (ENM) built from a given macromolecular structure Macromolecule Flexibility
LINK MoViES (Molecular Vibrations Evaluation Server) Macromolecule Flexibility
LINK DynDom is a program to determine domains, hinge axes and hinge bending residues in proteins where two conformations are available online, hinge, flexibility
LINK An Algorithm For Protein Hinge Prediction Using Elastic Network Models online, hinge, flexibility
LINK Flexweb: Analysis of Flexibility in Biomolecules and Networks online, hinge, flexibility
LINK TLS Motion Determination (TLSMD) analyzes a protein crystal structure for evidence of flexibility, e.g. local or inter-domain motions online, hinge, flexibility
LINK MOIL: Molecular Dynamics and Modeling Software standalone
LINK SQUEEZE is a method to reduce the computational cost of simulations of macromolecules performed under periodic boundary conditions. SQUEEZing allows removing the superfluous solvent molecules, by using the shape of the solute as the basis for the unit cell online
LINK CHARMM (Charmming) online for simulation, small molecules etc online
LINK OpenMM: open-source software that enables molecular dynamics (MD) simulations to be accelerated on high performance computer architectures .
LINK Ligandbook is a public repository for force field parameters for small drug-like molecules and known ligands of proteins .


URLs Virtual screening - Protein-ligand interactions, some aspects of chemical space Comments
LINK OAK Open Access Archive - Novartis Bioturbo Similarity Searching: Combining Chemical and Biological Similarity To Discover Structurally Diverse Bioactive Molecules A matrix of 170 million HTS-FP similarities between 18600 public compounds from ChEmbl data
LINK Dempster Shafer Theory (DST), A tool for the post data analysis of screened compounds derived from computer-aided docking scores online
LINK ChemMine tools: an online service for analyzing and clustering small molecules, similarity search online
LINK AuPosSOM: Automatic clustering of docking poses in virtual screening process using self-organizing map online
LINK The Molecule Cloud - compact visualization of large collections of molecules (P Erlt and B Rhode). Works with Avalon Cheminformatics Toolkit. http://sourceforge.net/projects/avalontoolkit/ standalone and ask the author
LINK Visualizing the words that characterize a text, online online
LINK MQN-Mapplet: Visualization of Chemical Space with Interactive Maps of DrugBank, ChEMBL, PubChem, GDB-11, and GDB-13 online and standalone
LINK MolClass: a web portal to interrogate diverse small molecule screen datasets with different computational models, MolClass thus defines a likelihood value for each compound entry and creates an activity fingerprint across diverse sets of screens online and standalone
LINK MolClass: A REST service is available based on the OpenTox API 1.2 .
LINK REPROVIS-DB: A Benchmark System for ligand-based virtual screening - Data sets datasets
LINK S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures database
LINK JACOB (just a collection of benchmarks): a dynamic database for computational chemistry benchmarking database
LINK Filter-it and related, software packages to filter collections and many others, pharmacophore, extract molecular scaffolds, align shape... standalone
LINK Xscore: scoring function online
LINK MiniMuDS: a new optimizer using knowledge-based potentials improves scoring of docking solutions (Dr Klebe s group) standalone and online
LINK e-Drug3D offers a facility to explore FDA approved drugs online
LINK DecoyFinder is a graphical tool which helps finding sets of decoy molecules for a given group of active ligands standalone
LINK RDock : is a very fast open source small molecule protein docking programme that was initially developed by Vernalis standalone
LINK Autogrow: Ligand design using fragment-based growing, docking, and evolutionary techniques standalone
LINK 3DFS is a program to search 3D databases for compounds matching a pharmacophore query Compound searching, needs password to get in
LINK LigMerge. Program combining structures of known binders to generate similar but structurally distinct compounds that can be tested for binding standalone
LINK LigCSRre 3D Ligand-Based virtual screening methods Ligand-based screening, online
LINK MoFa: Molecular fragment miner Compound searching, standalone
LINK MoSS - Molecular Substructure Miner. A program to find frequent molecular substructures and discriminative fragments in a database of molecule descriptions Compound searching, standalone
LINK ShaEP aligns (superimposes) two rigid 3D molecular structure models and computes a similarity index for the overlay standalone
LINK FTreesWeb Similarity search with Feature trees Similarity search online
LINK FTreesWeb and related similarity search - ligand-based screening
LINK many tools for chemistry docking ROCS-like tools, etc ADME Tox Cytochrome P450 site of metabolism....etc. Simtk.org is the home of the software framework initiated and developed by Simbios, the National NIH Center for Biomedical Computing focusing on Physics-based Simulation of Biological Structures Chemoinformatics - Toolkit, need to register
LINK Zodiac is a Molecular Modelling suite for drug design. Its features include support for haptic devices and nintendo wiimote fully undoable command list, MMFF94 implementation, POVRAY output Chemoinformatics - Toolkit, standalone
LINK LigBuilder: Based on the three-dimensional structure of the target protein, it can automatically build ligand molecules within the binding pocket Compound searching, ligand-based, standalone
LINK CONTACT THE AUTHORS OR GET THE APPLICATION IN THE SUPPL. systematic method to predict ligand-protein interactions, even for targets with no known 3D structure and few or no known ligands structure-based, ligand-based, biostatistics, standalone
LINK FINDSITELHM is a homology modeling approach to flexible ligand docking. It uses a collection of common molecule substructures derived from evolutionarily related templates as the reference compounds in similarity-based ligand binding pose prediction. It also provides a simple scoring function to rank the docked compounds standalone
LINK SurflexSim by Jain, VLS based on the ligand structure ligand-based screening, standalone
LINK PharmaGist: Predicting molecular interactions is a major goal in rational drug design Compound searching, ligand-based, Pharmacophore, online
LINK SAAMCO (Similarity of Amino Acid Motifs to Compounds) finds small molecules resembling peptides based on their side chains, many tools for peptides Compound searching, ligand-based, peptidomimetic, standalone
LINK Molprint2D, a fast fragment-based similarity searching method Compound searching, ligand-based, standalone
LINK USRCAT: real-time ultrafast shape recognition with pharmacophoric constraints Compound searching, ligand-based, standalone
LINK AURAmol allows a user to take a candidate 2D or 3D molecular shape and use it to search for similarly shaped molecules in large databases Compound searching online
LINK Graph Theoretical Similarity Approach To Compare Molecular Electrostatic Potentials. Similarity search, standalone
LINK MEssEM: A MOLECULAR QUANTUM SIMILARITY MEASURES SYSTEM OF PROGRAMS (Molecular Similarity: Methodological Development and Applications of Quantum Molecular Similarity Measures to Chemical Reactivity and analysis of Charge Density Distributions) Similarity search, standalone
LINK New Human GPCR modeling and virtual screening database is constructed using FINDSITEX GPCR modeling screening online
LINK SEED = Program for docking libraries of fragments with solvation energy evaluation; FFLD = Program for fragment-based flexible ligand docking; DAIM = Decomposition And Identification of Molecules; VLG = Virtual Library Generator Scoring Fragment Docking, standalone
LINK DOVIS: an implementation for high-throughput virtual screening using AutoDock. Zhang et al., BMC Bioinformatics. 2008 Feb 27;9(1):126 Small molecule docking, standalone
LINK GriDock The virtual screening front-end for AutoDock 4 Ligand_docking, standalone
LINK DockoMatic - Automated Ligand Creation and Docking. BMC Res Notes. 2010 Nov 8;3(1):289. Bullock CW, Jacob RB, McDougal OM, Hampikian G, Andersen T. Docking interface for Autodock, standalone
LINK myPresto is a molecular simulation system for structure-guided molecular development Small molecule docking - tools for screening - simulation, standalone
LINK SLITHER: a web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating through channels in membrane transporters Small molecule docking, online
LINK VSDocker: a tool for parallel high-throughput virtual screening using AutoDock on Windows-based computer clusters Small molecule docking - screening, server down ?
LINK BetaDock is a molecular docking simulation software based on the theory of Beta-complex. The authors claim that BetaDock is superior to any contemporary docking software while it requires less human intervention standalone
LINK pharmACOphore: The flexible superimposition of biologically active ligands is a crucial step in ligand-based drug design. Our new approach pharmACOphore for pairwise as well as multiple flexible alignment of ligands is based on ant colony optimization (ACO). An empirical scoring function is used, which describes ligand similarity by minimizing the distance of pharmacophoric features standalone
LINK Q-dock (coming soon) .
LINK DEKOIS: Demanding Evaluation Kits for Objective In silico Screening The datasets are derived from active sets that are available at the Directory of Useful Decoys datasets
LINK Score version 2 (Score calculator for molecular docking) online
LINK Ligscore: online scoring (pose and rank) between a ligand in mol2 and a protein online
LINK MotifScore: Using interaction network and motif to perform non-energy-based docking online
LINK BSP-SLIM low resolution small molecule docking on predicted structures online
LINK DockingServer offers a web-based, easy to use interface that handles all aspects of molecular docking from ligand and protein set-up online in part commercial, need to register
LINK MolShaCS: A free and open source tool for ligand similarity identification based on Gaussian descriptors standalone
LINK Server, screening with EADock Small molecule docking - screening, online
LINK MeDock, screening online
LINK AutoDock Vina plugin for PyMol standalone
LINK the new Autodock/Vina plugin for PyMOL standalone
LINK AutoDock and AutoDock Vina: Check here: http://vina.scripps.edu/ Small molecule docking - screening, standalone
LINK PARADOCKS: A Framework for Molecular Docking with Population-Based Metaheuristics. The source code is available Small molecule docking - screening, standalone
LINK Rosetta Ligand. Monte Carlo minimization procedure in which the rigid body position and orientation of the small molecule and the protein side-chain conformations are optimized simultaneously standalone
LINK Docking At UTMB. Web-driven interface for performing structure-based virtual screening with AutoDock Vina online
LINK HADDOCK (High Ambiguity Driven biomolecular DOCKing) is an approach that makes use of biochemical and/or biophysical interaction data such as chemical shift perturbation data resulting from NMR titration experiments, mutagenesis data or bioinformatic predictions. First developed from protein-protein docking, it can also be applied to protein-ligand docking online and standalone
LINK COPICAT. (COmprehensive Predictor of Interactions between Chemical compounds And Target proteins). System for predicting interactions between chemical compounds and proteins by using Support Vector Machine (SVM). COPICAT realizes comprehensive prediction of protein-chemical interactions by utilizing very general data i.e. amino acid sequences and chemical structures online
LINK BDT (is an easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock Interface for Autodock docking, standalone
LINK Dockres (reads the log file of docking runs performed by Autodock AutoDock post-docking processing, server down
LINK Information theory-based scoring. The tool could become available at Dr Richard Jackson' site Scoring
LINK eHits, commercial demo Small molecule docking - structure-based screening
LINK FRED small molecule docking. See the online demos to try many OpenEye applications Small molecule docking, commercial
LINK DOCK : Small molecule docking Small molecule docking standalone
LINK MS-DOCK Small molecule docking, works with DOCK, standalone
LINK ViewDock to analyze Dock data and tools for post-processing DOCK results, works with Chimera Small molecule docking post-docking processing, standalone
LINK PubDock, docking pubchem ligands (few targets have been done) Small molecule docking - structure_based_VLS, for now server is down, could work with Chimera
LINK MoSS - Molecular Substructure Miner fragmentation analysis of collections substructures, standalone
LINK SMIREP is a system for predicting the structural activity of chemical compounds. For that it can be categorized as a SAR/QSAR tool. The advantages of SMIREP are that it is failry fast, due to a heuristic approach of identifying the main features of active versus inactive compounds find key substructures, standalone
LINK ZINCPharmer: pharmacophore search of the ZINC database ZINCPharmer online
LINK Quantum.Ligand.Dock (protein-ligand docking with graphic processing unit (GPU) quantum entanglement refinement on a GPU system) online but does not seem to work
LINK GalaxyDock is a protein-ligand docking program that allows flexibility of pre-selected side-chains of ligand. Binary executible files (run on linux or MAC) and examples can be freely downloaded at the following link Small molecule docking - structure_based_VLS, standalone
LINK FITTED and see also FORECASTER Small molecule docking - structure_based_VLS, standalone
LINK Surflex: Small molecule docking Small molecule docking - structure_based_VLS, standalone
NO LINK ISE-dock: based on Autodock. Gorelik B, Goldblum A. Proteins: 2008 71:1373-86. Contact the authors Small molecule docking - structure_based_VLS, standalone
LINK AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening Small molecule pre-processing and post-docking processing, flexibility - induced-fit, standalone, but also online at mobyle RPBS
LINK CDOCK is a protein-ligand docking program similar to Autodock Small molecule docking - structure-based screening, standalone
LINK Plants (Korb et al. 2006): Small molecule docking. There is also a tool to prepare small molecules called SPORES Small molecule docking, standalone
LINK Pharmer: Pharmer is a pharmacophore search technology that can search millions of chemical structures in seconds standalone
LINK Open3DALIGN is an open-source software aimed at unsupervised molecular alignment standalone
LINK SwissDock: a web service to predict the molecular interactions that may occur between a target protein and a small molecule Small molecule docking, full surface screening possible, structure-based screening, online
LINK iScreen: cloud-computing web server for virtual screening and de novo drug design Small molecule docking - structure-based screening online
LINK 1-Click Docking 1 free docking online
LINK Sanjeevini : docking small molecules online
LINK DOCK Blaster Small molecule docking - structure-based screening online
LINK DockingServer Small molecule docking - structure-based screening online
LINK FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots FTFlex identifies flexible residues within the binding site and determines alternative conformations using a rotamer library online
LINK ParDOCK: An All Atom Energy Based Monte Carlo Docking Protocol for Protein-Ligand Complexes Small molecule docking, standalone
LINK Binding Affinity Prediction of Protein-Ligand (BAPPL) Small molecule scoring online
LINK Score. Allows to calculate some different docking scores of ligand-receptor complex that can be submitted as a whole file containing both interaction partners or as two separated files. The calculation phase is provided by VEGA Small molecule scoring online
LINK Bapplz: Binding Affinity Prediction of Protein-Ligand binding site with Zinc Small molecule scoring, online
LINK Drug Design tools Drug Design tools
LINK PSO at Autodock Small molecule docking, standalone
LINK Receptor based molecular docking (GlamDock) Small molecule docking - structure-based ligand-based screening, standalone
LINK PSI-DOCK: Small molecule docking. You may try ftp://ftp2.ipc.pku.edu.cn/pub/software Small molecule docking standalone
LINK PEARLS: Program for Energetic Analysis of Receptor-Ligand System Scoring online
LINK GFscore : A General Non-Linear Consensus Scoring Function for High-Throughput Docking Scoring standalone
LINK SCORE3 is an empirical method developed for estimating the binding affinity of protein-ligand complex with known three-dimensional structure. Possibly also at ftp://ftp2.ipc.pku.edu.cn/ Scoring standalone
LINK DrugScore (now DSX): evaluate ligand-receptor interaction energy Scoring, should be online
LINK FOLD-X can compute binding energy Scoring online
LINK CLIBE Computed ligand binding energy, A database for facilitating the analysis of Drug Binding Competitveness Help for scoring online
LINK Scoring using molecular interaction fingerprints - package available upon request to Dr. D. Rognan or directely from the website, also online at RBPS mobyle Scoring via molecular interaction fingerprints
LINK HINT Scoring standalone
LINK Tools to build molecular-docking activity prediction models by PLS regression with iterative training and pose-selection. Descriptors include (i) docking score(s), (ii) pharmacophore features, (iii) multi-feature descriptors learned by decision trees Scoring standalone
LINK HBAT(Hydrogen Bond Analysis Tool) is a tool to automate the analysis of hydrogen bonds present in a PDB Structure file. Other related tools available from HBAT Project are PDIA(Post Docking Interaction Analysis) and HBNG(Hydrogen Bond Network Graph) Post-docking analysis standalone
LINK Xscore : tool to predict binding energy between ligand and receptor Scoring standalone
LINK The goal of the http://www.cgal.org/opensource_frame.html CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms to users in industry and academia in the form of a C++ library Help for docking
LINK datasets for FXa, ADMET.. for docking... download
LINK GEMSTONE (Grid Enabled Molecular Science Through Online Networked Environments) Tools to speed-up computations
LINK BioDrugScreen. Computational drug design and discovery resource and server. The portal contains the DOPIN (Docked Proteome Interaction Network) database constituted by millions of pre-docked and pre-scored complexes from thousands of targets from the human proteome and thousands of drug-like small molecules from the NCI diversity set and other sources. The portal is also a server that can be used to (i) customize scoring functions and apply them to rank molecules and targets in DOPIN; (ii) dock against pre-processed targets of the PDB; and (iii) search for off-targets. Structural Protein-Ligand Interactome (SPLINTER) online
LINK Kindock and Simdock Tool for comparative docking of protein kinase ligands and ligand transposition server Small molecule positioning, online
LINK Small molecule positioning, online
LINK Arguslab: A molecular modeling, graphics, and drug design program. Performs fast shape docking like FRED and has tools similar to AutoDock. Problems so far, it runs only on Windows Molecular docking, standalone
LINK The Ligand Explorer Java Tools for interactive post-processing of docking studies, standalone
LINK Many computer tools for small (or large) molecules Tools for docking and small molecules by Dr. Michel Petitjean, standalone
LINK LIGPLOT = Program for automatically plotting protein-ligand interactions Tools to view active site, standalone
LINK PoseView automatically creates two-dimensional diagrams of complexes Tools to view active site, online
LINK ROCR is an R package (http://www.r-project.org/) for evaluating and visualizing classifier performance. See tutorials about ROC curve: http://www.anaesthetist.com/mnm/stats/roc/Findex.htm; http://nicolaorsini.altervista.org/stata/tutorial/r/tu_rocss.htm; http://pops.csse.monash.edu.au/roccurves_doc.html; http://www.mlahanas.de/MOEA/Med/ROC21.htm Analyzing results of virtual screenings: ROC curves, standalone
CoLiBRI Chemometric analysis of ligand receptor complementarity. Need to contact the authors, J Chem Inf Model 2006, 46, 844-851 Fast reduction of the compound collection
LINK PROFEAT- Protein Feature Server for computing physicochemical properties of proteins and peptides from their primary sequences Protein Feature Server - SVM, online
LINK ProtParam is a tool which allows the computation of various physical and chemical parameters for a given protein stored in Swiss-Prot or TrEMBL or for a user entered sequence. The computed parameters include the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY) for SVM - protein parameter, online
LINK Ligand Validator at Uppsala University: ValLigURL online
LINK PyPLIF: Python-based Protein-Ligand Interaction Fingerprinting standalone
LINK Pose and Rank : a web server for scoring protein-ligand complexes (Sali lab) online
LINK The CaPTURE program can identify energetically significant cation-pi interactions within proteins online
LINK X-score online
LINK I-interpret: uses standard geometry information about small ligands, like a ligand present in a PDB file and performs automatic atom/bond-type assignment. It can takes several compounds at a time and propose protonation state. See Zhao, Cheng and Wang, J Chem inf Model in press 2007. Title: automatic perception of organic molecules based on essential structural information online
LINK Compute ligand-protein interaction energy after energy minimization performed by the package PLOP, protein local optimization program standalone
LINK McMaster Canada, HTS-VLS competition, does not seem to work April 17 2013 HTS-VLS competition, datasets
LINK The Molecular Libraries Screening Centers Network (MLSCN) consists of 10 centers with a diverse set of screening platform technologies that include ultraHTS, cell based imaging, and flow cytometry.. NIH USA project on screening .
LINK jCompoundMapper: An Open Source Java Library and Command-Line Tool for Chemical Fingerprints (standalone) .
LINK Alice: artificial intelligence foundation Artificial Intelligence, standalone, borderline with this topic
LINK SoftDB is a simple software database with a web interface designed to serve the needs of a particular field of research, in this case, structural biology. Since the scope of application is much more limited than similar systems such as freshmeat.net, the database and interface are relatively small, and can be run on almost any web server through the use of a few Perl scripts and a MySQL back-end database. data flows (often referred to as pipelines), standalone
LINK VSDMIP is a platform for virtual screening (VS) of chemical libraries, integrated within a MySQL relational database. Virtual screening, structure-based screening. See also cdock pipelines, standalone
LINK Open Source Molecular Modelling Workflow Environment. SOMA2 data flows, standalone
LINK KNIME data flows, standalone
LINK The Taverna project aims to provide a language and software tools to facilitate easy use of workflow and distributed compute technology within the eScience community data flows, standalone
LINK XBaya A Graphical Workflow Composer for Web Services Data flows, standalone
LINK ChemGPS-NP Web - A tool tuned for navigation in biologically relevant chemical space Chemical Space, Chemoinformatics, online
LINK SARANEA is a freely available program to mine structure-activity and structure-selectivity relationship information in compound data sets, activity cliff. Bajorath et al. J. Chem. Inf. Model., 2010. Also several compound collections for hERG, proteases... Chemoinformatics, standalone
LINK ScaffoldTreeGenerator Chemoinformatics - navigation in chemical space, standalone
LINK Scaffold Hunter, Interactive exploration of chemical space Chemoinformatics - navigation in chemical space, standalone
LINK Using as input the 3D structure of a peptide bound to a protein, pepMMsMIMIC suggests which chemical structures are able to mimic the protein-protein recognition of this natural peptide using both pharmacophore and shape similarity techniques (Swimming into peptidomimetic chemical, NAR 2011) Chemoinformatics - navigation in chemical space, online
LINK NNScore. Python script for computing binding free energies from PDBQT files of the receptor and the ligand, using a neural network approach standalone
LINK DrugScore replaced by the new scoring function DSX online
LINK BAPPL-Z: Binding Affinity Prediction of Protein-Ligand complex containing Zinc online
LINK Predict DNA-Drug Interaction strength online
LINK IC50-to-Ki converter online
LINK IC50-to-Ki converter online
LINK de novo drug design engine to create new molecules either from scratch (lead-hopping) or based on a user-defined scaffold on which R-groups have to be optimized (Douguet) online
LINK SwissBioisostere database database
LINK Pharmer is a pharmacophore search technology standalone
LINK GOMoDo (GPCR Online Modeling and Docking) provides a single web interface and pipeline to model GPCRs and to dock molecules into the model online


URLs Mutations, you may want to see also Simulation Comments
LINK iStable: off-the-shelf predictor integration for predicting protein stability changes online stability change, input PDB or sequence, stability
LINK PASE: a novel method for functional prediction of amino acid substitutions based on physicochemical properties (Python and Biopython, Unix Linux) standalone
LINK GREMET: An integrative tool for the prediction of mutation effects on gene regulation online
LINK HCMV tool linking human cytomegalovirus drug resistance mutations to resistance phenotypes online
LINK SDM requires a PDB file of the wild-type protein structure in order to calculate a stability score for mutant proteins. If you do not have a PDB structure ready for input, the tool proposes to assist you in finding one online stability change
LINK The SCHEMA energy function, RASPP, uses structural information to predict which fragments of proteins can be swapped without disrupting the integrity of the three-dimensional structure Mutation, protein stability, standalone
LINK COREX/BEST server: a web browser-based program that calculates regional stability variations within protein structures Protein regional stabilities, online, need to register
LINK PON-P, Pathogenic-or-Not -Pipeline, PON-P is a machine learning-based method for predicting whether variants affect functions and thereby lead to diseases. PON-P portal allows submission and prediction into altogether 31 distinct tools. The current version analyses only missense variations i.e. amino acid substitutions. online, input sequences
LINK VariBench: A benchmark database for variations database
LINK VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations standalone
LINK Cmat: Reliable and robust detection of coevolving protein residues online and standalone
LINK DFire2: Scoring Protein Conformational Free Energy online
LINK Automute: AUTOmated server for predicting... ...functional consequences of amino acid MUTations in protEins online, stability change, input PDB
LINK Prediction of Protein Stability Changes (PPSC) standalone
LINK SNAP is a method for evaluating effects of single amino acid substitutions on protein function online, input sequence
LINK Panther, SNP Analysis : Estimates the likelihood of a particular nonsynonymous (amino-acid changing) coding SNP to cause a functional impact on the protein. It calculates the subPSEC (substitution position-specific evolutionary conservation) score based on an alignment of evolutionarily related proteins online, input sequences
LINK PEATSA webserver predicts the effect of mutations on a number of properties of a protein, it is a part of the PEAT suite online stability change and others, several input including ligand in mol2
LINK I-Mutant2.0, stability change online, input sequences or PDB
LINK SCCOMP is a program for side chain modeling online
LINK SRide: Identification of Stabilizing Residues in proteins, stability changes online structural analysis, input PDB
LINK The goal of MutDB is to annotate human variation data with protein structural information and other functionally relevant information, if available online, keywords as input
LINK FoldX: provide a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes online, stability change
LINK TANGO : predict protein aggregation online, aggregation
LINK SIFT (sorting intolerant from tolerant): predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids online, standalone and online, input sequence
LINK Parepro (Prediction of amino acid replacement probability) is a method of identifying which non-synonymous single base changes have a deleterious effect on protein function, based on support vector machine (SVM). As an input it requires the protein sequence and other protein sequences homologous to it online
LINK MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins online disorder
LINK ESpritz: accurate and fast prediction of protein disorder online disorder
LINK aggrescan Prediction of hot spots of aggregation in polypeptides online aggregation
LINK Aggregation Prediction with PASTA online aggregation
LINK MolProbity: all-atom contacts and structure validation for proteins and nucleic acids online structural analysis
LINK Diseasome: an integrated database of Genes, Genetic variation, and Diseases online, search by keywords and codes
LINK Clustal Omega is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments (replace Clustal-W2) online, multiple seq alignment
LINK MUSCLE stands for MUltiple Sequence Comparison by Log- Expectation. MUSCLE is claimed to achieve both better average accuracy and better speed than ClustalW2 or T-Coffee, depending on the chosen options online multiple seq alignment
LINK MISTRAL (Multiple STRuctural ALignment) is a novel strategy for multiple protein alignment based on the minimization of an energy function over the low-dimensional space of the relative rotations and translations of the molecules online, input PDB
LINK T-Coffee Server A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures online multiple seq alignment
LINK Dmutant: Mutation Stability Change Prediction online, input PDB file
LINK Bluues server: electrostatic properties of wild-type and mutated protein structures Electrostatics, online, input PDB
LINK Align-GVGD is a freely available, web-based program that combines the biophysical characteristics of amino acids and protein multiple sequence alignments to predict where missense substitutions in genes of interest fall in a spectrum from enriched delterious to enriched neutral. Align-GVGD is an extension of the original Grantham difference to multiple sequence alignments and true simultaneous multiple comparisons. Users can either supply their own protein multiple sequence alignments (in FASTA format) or else select from our small but growing library of alignments online needs sequences
LINK mCluster uses a comprehensive collection of somatic mutations, germline disease mutations and other information to identify key residues in conserved protein domains which are enriched for mutations online needs gene or protein name
LINK LS-SNP is a web tool for genome-wide annotation of human SNPs The current version, LS-SNP/PDB, provides information useful for identifying amino-acid changing SNPs (nsSNPs) that are most likely to have an impact on biological function search can be by PDB code, gene, UniProt, dbSNP rs ID online
LINK nsSNPAnalyzer: predicting disease-associated nonsynonymous single nucleotide polymorphisms online, needs sequences, option also 3D data
LINK Hansa: an automated method for discriminating disease and neutral human nsSNPs online mutation analysis, input seq
LINK FATHMM Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models Using a model weighted for human mutations, we obtained performance accuracies that outperformed traditional prediction methods (i.e., SIFT, PolyPhen, and PANTHER) on two separate benchmarks. Furthermore, in one benchmark, we achieve performance accuracies that outperform current state-of-the-art prediction methods (i.e., SNPs and GO and MutPred) online mutation analysis, sequence
LINK PhD-SNP Predictor of human Deleterious Single Nucleotide Polymorphisms online mutation analysis, as input it requires protein sequence and the position of the SNP
LINK Protein frustratometer: a tool to localize energetic frustration in protein molecules. Frustration is a useful concept for gaining insight to the proteins biological behavior by analyzing how the energy is distributed in protein structures and how mutations or conformational changes shift the energetics. Sites of high local frustration often indicate biologically important regions involved in binding or allostery. In contrast, minimally frustrated linkages comprise a stable folding core of the molecule that is conserved in conformational changes online analysis
LINK PharmGKB is a comprehensive resource that curates knowledge about the impact of genetic variation on drug response for clinicians and researchers database
LINK HUMSAVAR: common polymorphism variants and mutations annotated in UniProt database
LINK Pro-Maya (Protein Mutant stAbilitY Analyzer): Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site online mutation analysis
LINK ASAVIEW: server provides graphical representation of solvent accessibility of amino acid residues in proteins, with known structures online mutation analysis
LINK UTRscan is a pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA) sequences in order to find UTR motifs (Each UTRsite entry is constucted on the basis of information reported in the literature and revised by scientists experimentally working on the functional characterization of the relevant UTR regulatory element) online mutation analysis
LINK tools to analyze genes, Gene evaluator, gene predictor, gene translator, melting point temperature predictor, non coding RNA database online gene analysis and databases
LINK PASE: a novel method for functional prediction of amino acid substitutions based on physicochemical properties standalone mutation analysis
LINK PolyPhen-2 online mutation analysis
LINK ProCon: localization and visualization of Protein Conservation standalone, mutation
LINK PROlocalizer - integrated web service for protein subcellular localization prediction online
LINK RankViaContact is a web service for calculation of residue-residue contact energies in proteins based on a coarse-grained model and for visualisation of interactions (Shen and Vihinen) online
LINK MultiDisp is a tool for visualisation of multiple sequence alignments online
LINK FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization. FASTSNP (function analysis and selection tool for single nucleotide polymorphisms) is a web server that allows users to efficiently identify and prioritize high-risk SNPs according to their phenotypic risks and putative functional effects. A unique feature of FASTSNP is that the functional effect information used for SNP prioritization is always up-to-date, because FASTSNP extracts the information from 11 external web servers at query time using a team of web wrapper agents online
LINK ProTherm is a collection of numerical data of thermodynamic parameters such as Gibbs free energy change, enthalpy change, heat capacity change, transition temperature ... for wild type and mutant proteinsonline database
LINK Mutation Assessor (before Xvar): The server predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms online, sequences
LINK MutaProt: Comparison of PDB files which differ by point mutations online standalone
LINK Monster inferring potentially stabilizing non-bonding interactions in macromolecular structures online
LINK DisEMBL prediction of disordered/unstructured regions online
LINK Disopred2 Predictor of Intrinsically Disordered Regions online, disorder
LINK AVP (Another Void Program) for the analysis of voids in proteins and packing quality standalone
LINK PMut combines sequence alignment/PSSM with structural factors to characterize missense substitutions. given a mutation happening at a specific location in a protein sequence, can we say whether it can be pathological (that is, it can lead to disease for the carrier) or non-pathological/neutral (no effect on the carrier's health)? online
LINK SNPeffect 4 online search keywords
LINK SNPs3D, based on sequence and structure online
LINK PicSNP catalog of non-synonymous SNP in the human genome data
LINK topoSNP : This site produces an interactive visualization of disease and non-disease associated non-synonymous single nucleotide polymorphisms (nsSNPs) and displays geometric and relative entropy calculations online PDB code
LINK Analysis of correlated mutations .
LINK Eris: predict impact of mutation, stability online, input PDB, need to register
LINK CUPSAT predicts changes in protein stability upon point mutations online
LINK MUpro : Prediction of Protein Stability Changes for Single-Site Mutations from Sequences online, mutation
LINK PoPMuSiC, an algorithm for predicting protein mutant stability changes online, mutation
LINK CPred: Circular permutation (CP) of protein is an evolutionary event resulting in the fact that structural homologs may have different locations of termini. It can be visualized as if the original termini of a protein were linked and new ones created elsewhere online, PDB code
LINK XRNAmute online for RNA
LINK pKD: This server lets you pick a PDB file, specify how much and in which direction you want to change a pKa value of a titratable group in this protein, and subsequently the server calculates a set of point mutations that will cause the desired pKa change online
LINK Hint Hydropathic INTeractions commercial
LINK KD4v: comprehensible knowledge discovery system for missense variant: The goal of KD4v server is to study and understand the links between the structural impact of a mutation and the human disease phenotype online
LINK mutationassessor : The server predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms online
LINK Condel is a method to assess the outcome of nonsynonymous SNVs using a consensus deleteriousness score that combines various tools (e.g. SIFT, Polyphen2, MutationAssessor) online
LINK wKinMut is an integrated framework for the analysis of kinase mutations online
LINK SNPnexus: a web server for functional annotation of novel and publicly known genetic variants online
LINK FoldX provides a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes mutation, online


URLs Display molecules - Visualization of information Comments
LINK BiologicalNetworks backend database (IntegromeDB) integrates >1000 curated data sources (from the NAR list) for thousands of eukaryotic, prokaryotic and viral organisms and millions of public biomedical, biochemical, drug, disease and health related web resources, molecules in 3D... standalone
LINK JSME is a conversion of the popular JME applet to JavaScript (B. Bienfait and P. Ertl). JSME supports drawing and editing of molecules and reactions on desktop computer. The applet can also serve as a query input tool for searching molecular databases by supporting creation of complex substructure queries, which are automatically translated into SMARTS standalone and online
LINK Arena3D Visualizing biological networks in 3D standalone
LINK BioLayout Express3D is a powerful tool for the visualization and analysis of network graphs standalone
LINK PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization online
LINK Ondex Data integration and visualisation standalone
LINK Osprey Network Visualization System standalone
LINK Gephi The Open Graph Viz Platform standalone
LINK VisANT, visual analysis tool for biological networks and pathways online and standalone
LINK Graphviz - Graph Visualization Software standalone
LINK MQN-Mapplet: Visualization of Chemical Space with Interactive Maps of DrugBank, ChEMBL, PubChem, GDB-11, and GDB-13 online and standalone
LINK UnityMol: Using the Unity3D game engine to create a molecular viewer and serious games standalone
LINK VAST, short for Vector Alignment Search Tool, is a computer algorithm developed at NCBI and used to identify similar protein 3-dimensional structures by purely geometric criteria, and to identify distant homologs that cannot be recognized by sequence comparison online
LINK The Human Protein Atlas (HPA) is a powerful repository of protein expression patterns in human anatomical structures in normal and diseased tissues, accessible over the Web online
LINK ProPhylER is a tool for visualizing the evolutionary constraints that have influenced a protein, as inferred from comparative analyses of closely related proteins sequences. Most interestingly, it can display the degree of evolutionary pressure experienced by different regions of a protein online
LINK FirstGlance in Jmol:A simple tool for macromolecular visualization online online
LINK DAVID, the Database for Annotation, Visualization And Integrated Discovery system, is a free, publicly-accessible web-based suite of tools for analyzing microarray gene expression results using the metadata properties (i.e., annotations) of a list of genes and their cognate proteins online
LINK CDTree is an integrated suite of software tools for analyzing sequences from protein domains curated in NCBI's Conserved Domains Database (CDD) in the context of domain family hierarchies online
LINK Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of plugins are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web standalone
LINK IntAct provides a freely available, open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions and are freely available online
LINK GeneMANIA is a flexible, user-friendly web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays online
LINK FLink is a tool that enables you to traverse from a group of records in a source database (e.g., Proteins) to a ranked list of associated records in a destination database (e.g., BioSystems) online
LINK MovieMaker online
LINK JKlustor small molecules
LINK Molprime small molecules - Phone app
LINK JChemPaint small molecules
LINK Bkchem small molecules
LINK Molinspiration small molecules
LINK Xdrawchem small molecules
LINK iMoledraw small molecules - Phone
LINK Sketchel small molecules
LINK Chemtool small molecules
LINK Bioclipse small molecules
LINK jsmoleditor small molecules
LINK ketcher small molecules
LINK chemwriter small molecules
LINK molinspiration small molecules
LINK chemaxon small molecules
LINK chemicalize chemaxon online
LINK The SMARTSviewer generates a visualization of a SMARTS string online
LINK Jamberoo - cross platform molecular editor .
LINK The PubChem chemical structure sketcher, get SMILES and SMARTS online
LINK OSRA (Optical Structure Recognition Application) is a utility designed to convert graphical representations of chemical structures and reactions, as they appear in journal articles, patent documents, textbooks, trade magazines etc. standalone
LINK OSRA online (Optical Structure Recognition Application) Images to SMILES, online
LINK OSRA: Optical Structure Recognition, take the 2D drawing of a compound and get the SMILES Images to SMILES
LINK MolviZ.Org To display and rotate macromolecules and small molecules in a single internet browser Molecular graphics
LINK Cn3D: displays structures of macromolecules and performs sequence alignments Molecular graphics
LINK DINO : 3D viewer essentially for macromolecules .
LINK DisMol: Java applet viewer for macromolecules and small molecules .

LINK

 MolScript .
LINK Colorado3D web server for the visual analysis of protein structures online
LINK Pymol .
LINK LigAlign: The same ligand is likely to bind different proteins in similar, instructive ways. This tool automates comparisons of such active sites. This is a PyMOL-based structure visualization tool which utilizes ligand-based active site alignment. .
LINK BioJS: an open source JavaScript framework for biological data visualization standalone
LINK NAViGaTOR - Network Analysis, Visualization, & Graphing TORonto is a software package for visualizing and analyzing protein-protein interaction networks .
LINK VMD Molecular graphics, structural analysis
LINK MolWorks: graphic tool for drawing and sketching molecules .
LINK ChemSpotlight: metadata importer pluging for Mac OS X, which reads common chemical file formats (PDB, Mol2, SDF...) .
LINK ICM browser Molecular graphics
LINK OpenEye Vida Molecular graphics
LINK PovChem is a chemical visualization and illustration program Molecular graphics, structural analysis
LINK With gOpenMol allows visualization and analysis of small molecules Molecular graphics
LINK KMovisto is a 3D molecule viewer essentially for Linux Molecular graphics
LINK YASARA Molecular graphics and modeling
LINK Molegro viewer .
LINK UCSF Chimera .
LINK Open source molecule viewer Jmol .
LINK Links to protein crystallography tools such as CCP4, etc .
LINK Xemistry Web Sketcher Demonstration online
LINK
LINK 		FirstGlance in Jmol, a simple tool for macromolecular visualization (installed online at these sites) Graphics, Molecular Modeling
LINK jAMVLE: jmol Amalgamated Molecular Visualization Learning Environment Graphics
LINK Molecular graphics - Astex .
LINK The PSI3 suite of quantum chemical programs ab initio quantum chemistry package
LINK Protein movie generator online
LINK Vega ZZ .
LINK Avogadro .
LINK Rasmol .
LINK Cosmos .
LINK bioadviser .
LINK BINANA (BINding ANAlyzer). Python-implemented algorithm for analyzing ligand binding
LINK Yet Another extended Huckel Molecular Orbital Package (YAeHMOP), freely available extended Huckel calculation and visualization package standalone
LINK Accelrys software: structural bioinformatics, drug design and related (e.g., Pipeline) commercial
LINK Molecular Discovery commercial
LINK Schrodinger software: structural bioinformatics, drug design and related (e.g, Glide) commercial
LINK MOE software: structural bioinformatics, drug design and related commercial
LINK Inte:Ligand drug design and related commercial
LINK Biosolveit software: structural bioinformatics, drug design and related commercial
LINK OpenEye software: drug design commercial
LINK Stardrop software: drug design commercial
LINK GUSAR is a tool to create and use models on quantitative structure-activity relationships (QSAR) Windows commercial
LINK hint is a novel empirical molecular modeling system with new methods for de novo drug design and protein or nucleic acid structural analysis standalone
LINK Cresset software: drug design commercial
LINK Medit software: drug design commercial
LINK Molsoft: software, structural bioinformatics, drug design and related commercial
LINK Tripos software: structural bioinformatics, drug design and related commercial
LINK Molinspiration software: drug design commercial
LINK Daylight software: drug design commercial
LINK Chemaxon software: drug design commercial


URLs Peptides, antibodies, epitopes Comments
LINK FOBIA: FOlding By hIerarchical Assembly online
LINK Superficial : approach to design peptide librairies that mimic the surface of a protein online
LINK VaccImm Server that allows users to simulate peptide vaccination in cancer therapy. It uses an agent-based model that simulates peptide vaccination by explicitly modelling the involved cells (immune system and cancer) as well as molecules (antibodies, antigens and semiochemicals) online
LINK MSPeptider, a web tool to predict the cross-section area of peptides from its primary sequence of amino acids online
LINK Quorumpeps database: chemical space, microbial origin and functionality of quorum sensing peptides online
LINK CrossTope: a curate repository of 3D structures of immunogenic peptide: MHC complexes online
LINK CBS Prediction Servers: numerous tools to analyze protein sequences, Post-translational modifications of proteins, Protein function and structure: BepiPred DiscoTope HLArestrictor NetChop NetCTL NetCTLpan NetMHC NetMHCcons NetMHCII NetMHCIIpan NetMHCpan NNAlign (Identifying sequence motifs in quantitative peptide data) VDJsolver Immunological features and many other tools online
LINK SolyPep: Random peptide library generation, accounting or not for solubility, and preparing for docking online
LINK PepMapper: a collaborative web tool for mapping epitopes from affinity-selected peptides online
LINK CSA: comprehensive comparison of pairwise protein structure alignments online
LINK Super: a web server to rapidly screen superposable oligopeptide fragments from the protein data bank online
LINK Monte Carlo simulations of peptide-membrane interactions with the MCPep web server online
LINK Paratome: an online tool for systematic identification of antigen-binding regions in antibodies based on sequence or structure online
LINK iAMP-2L: A two-level multi-label classifier for identifying antimicrobial peptides and their functional types online
LINK MESSA: MEta-Server for protein Sequence Analysis online
LINK Scaffold: A structural bioinformatics approach for identifying proteins predisposed to bind linear epitopes on pre-selected target proteins online
LINK Mutator: Improving the selectivity of antimicrobial peptides from anuran skin online
LINK GibbsCluster : Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach online
LINK SVMTriP : predict antigenic epitopes (Realistic prediction of protein surface regions that are preferentially recognized by antibodies (antigenic epitopes) can help the design of vaccine components and immuno-diagnostic reagents) online
LINK PepSite : prediction of peptide-binding sites online docking
LINK CellPPD: Designing of Cell Penetrating Peptides online
LINK ElliPro: Antibody Epitope Prediction online
LINK Pepitope : epitope mapping using affinity-selected peptides online
LINK PepMapper seems to outperform MimoPro or Pep-3D-Search. PepMapper is another multipurpose mapping tool for epitope prediction from affinity-selected peptides online
LINK BriX database of protein fragments. Loop BriX contains loop fragments from 14.525 proteins. database
LINK RosettaAntibody: antibody variable region homology modeling server online
LINK The Abysis antibody database integrates sequence data from Kabat, IMGT and the PDB with structural data from the PDB Antibody database
LINK DOMINO is an open-access database comprising more than 3900 annotated experiments describing interactions mediated by protein-interaction domains online database
LINK pepMMsMIMIC: using as input the 3D structure of a peptide bound to a protein, pepMMsMIMIC suggests which chemical structures are able to mimic the protein-peptide recognition of this natural peptide using both pharmacophore and shape similarity techniques (Swimming into peptidomimetic chemical, NAR 2011) peptides to chemical via screening online
LINK POW: structure-based predictor of PDZ domain-peptide interactions online
LINK BHAGEERATH-H: A Homology ab-intio Hybrid Web server for Protein Tertiary Structure Prediction online
LINK BHAGEERATH : An Energy Based Protein Structure Prediction Server online
LINK Standardizing and simplifying analysis of Peptide library data standalone
LINK Standardizing and simplifying analysis of Peptide library data online
LINK Innovagen's peptide calculator makes calculations and estimations on some physiochemical properties online peptide physchem
LINK PEP-FOLD (pepfold) prediction of the 3D structure of peptides, linear and cyclic online
LINK PeptideLocator: prediction of bioactive peptides in protein sequences online, need at present a UniProt IDs as input for the computation
LINK Haddock to predict peptide-protein interaction (peptides recognize hot spot (see Stein and Aloy, PLoS One 3: e2524, 2008). Peptide binding sites can be predicted by tools such as PepSite (see also Ben-Shimon, Eisenstein, 2010, J Mol Biol 402: 259–277). Haddock is compared to DynaDock and the FlexPepDock webserver (see Trellet et al., PLoS One. 2013;8(3):e58769) standalone and online
LINK PepBank is a database of peptides based on sequence text mining and public peptide data sources. Only peptides that are 20 amino acids or shorter are stored database
LINK PEPsolubility, predict peptide solubility online
LINK OPM database and PPM web server: resources for positioning of proteins in membranes online, can also be interesting to design peptides
LINK Rosetta FlexPepDock: The input for this server is a PDB file of a complex between a protein receptor (first chain) and an estimated conformation for a peptide (second chain). FlexPepDock was shown to be able to accurately refine the peptide structure starting from up to 5.5A RMSD of the native conformation, allowing full flexibility to the peptide and side-chain flexibility to the receptor online
LINK PEPstr : predict the tertiary structure of small peptides online
LINK ProBuilder, build a sequence in 3D online
LINK AVPpred antiviral peptides, also allow to get several properties of a sequence, polar, possible 3D structure, physchem etc online
LINK Super: screen superposable oligopeptide fragments from the protein data bank online
LINK PepMake generates a PDB coordinate file for polypeptide backbones using only the sequence and backbone dihedral angles as input online
LINK MODPROPEP: knowledge-based modeling of protein-peptide complexes standalone
LINK DILIMOT: for finding short (3-8 amino acids), over-represented peptide patterns online discovery linear motifs
LINK SLiMDisc (Short Linear Motif Discovery): find shared motifs in proteins with a common attribute such as sub-cellular location or a common interaction partner online
LINK the Bioware webserver contains several tools for short linear motif discovery and peptide characterisation. CycloPsWeb with logP, etc, PeptideRanker, PeptideLocator online
LINK PepX contains many unique protein-peptide interface from the PDB. February 2013, it contains 505 unique protein-peptide interface clusters from 1431 PDBs database
LINK PepCrawler high-resolution refinement and binding affinity estimation of peptide inhibitors online
LINK PepServe: a web server for peptide analysis, clustering and visualization online
LINK PeptideMine : a webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes online, PPI
LINK IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins. IBIS provided annotations for 5 different types of binding partners: proteins, PPI, small molecules, nucleic acids and peptides and ion online, also binding site
LINK ParDOCK: Protein-Ligand Complexes, might dock peptides (it is an all-atom energy based Monte Carlo,rigid protein ligand docking, implemented in a fully automated, parallel processing mode which predicts the binding mode of the ligand in receptor target site) online
LINK PROFEAT- Protein Feature Server for computing physicochemical properties of proteins and peptides online


URLs Teaching & training, Tutorials, Learning about file formats Comments
LINK International Master in drug design training
LINK Successfully navigating through the jungle of biomedical postgraduate courses in Europe has recently been made possible by the release of an Innovative Medicines Initiative (IMI) funded project called on-course training
LINK PhD in Systems Biology, Spain training
LINK David J. Wild Director, Cheminformatics Program, Indiana chemoinformatics
LINK Prof Willett, University of Sheffield chemoinformatics
LINK The Drug Discovery Resources section, CambridgeMedchemConsulting, Dr Chris Swain (medicinal chemist) drug discovery overview with the different steps nice online free reading
LINK Macs in chemistry, Chris Swain links .
LINK Prof Robert B. Russell, overview of amino acids in proteins, mutations... chemoinformatics
LINK Small chemistry quiz for fun
LINK Software for Atomic Scale Education & Research software for education
LINK short overview of the drug discovery process for small molecules and biologics quick view over drug discovery
LINK Tutorial for SMILES, SMARTS and chemistry toolkit SMILES format (Chemistry)
LINK Mol2 file format
LINK PDB file .
LINK SDF file .
LINK MMFF validation suite Simulation tools
LINK IUPAC International Chemical Identifier project Chemistry tools
LINK Information about different chemical structure file formats including SDF. (Dalby et al. J. Chem. Inf. Comput. Sci, 32, 244-255, 1992) Chemistry tools
LINK Educational Sources from the Internet online courses
LINK Course chemoinformatics J. Aires de Sousa Research Group Chemo courses
LINK Models of main functional groups, courses in organic chemistry Chemistry courses
LINK Molecular Models - Dave Woodcock Chemistry courses
LINK Master Chemoinformatics .
LINK Course chemoinformatics Denmark .
LINK Some chemical groups .
LINK About 900 Weblinks for Chem(o)informatics, Molecular Modeling from Dr Sung Kwang (free and commercial in silico tools and databases), Japan .
LINK Some rings .
LINK Most frequent scaffolds in FDA approved drugs .

URLs Modeling loops Comments
LINK SA-Mot: a web server for the identification of motifs of interest extracted from protein loops online
LINK BriX database of protein fragments. Loop BriX contains loop fragments from 14.525 proteins. database
LINK ArchPRED template based loop structure prediction server online
LINK FALC-Loop: protein loop modeling online
LINK ModLoop: Protein loop prediction online
LINK RigidFinder: detect rigid blocks in large macromolecular complexes online
LINK RosettaAntibody: antibody variable region homology modeling server online
LINK SuperLooper a prediction server for the modeling of loops in globular and membrane proteins, see also 2 databases: Loop in proteins (LIP) and LIMP (Loops In Membrane Proteins) at this site online

URLs Other links Comments
LINK The BioMart project provides free software and data services to the international scientific community in order to foster scientific collaboration and facilitate the scientific discovery process .
LINK The Mouse Genome Database: Genotypes, Phenotypes, and Models of Human Disease .
LINK prolific protein-literature investigation for interacting compounds .
LINK PHISTO: Pathogen-Host Interaction Search Tool online
LINK Bad bugs, no drugs. The infectious disease society of America (IDSA) online
LINK The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) as a measuring unit have become the gold standard for international drug utilization research. WHO Collaborating Centre for Drug Statistics Methodology online
LINK DisGeNET is a new gene-disease database integrating gene-disease associations from several public, expert, curated data sources and text mining derived associations online
LINK BioLabeler extracts UMLS concepts from Biomedical texts such as scientific paper abstracts, experiments descriptions or medical notes and can be use to automatically curate and annotate BioMedical Literature or to index large documents databases and improve searches or discover relationships between them .
LINK Biomine integrates and indexes data from several publicly available biological databases with the aim of aiding explorative discovery of non-trivial connections between biological entities, such as genes and phenotypes online
LINK PubTator is a Web-based tool for accelerating manual literature curation (e.g. annotating biological entities and their relationships) through the use of advanced text-mining techniques .
LINK OSCAR (Open Source Chemistry Analysis Routines) is an open source extensible system for the automated annotation of chemistry in scientific articles .
LINK PIE: Searching PubMed literature for protein interaction information .
LINK PRO provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them (target) .
LINK KiPar is a standalone Java application for the retrieval of textual documents likely to contain information relevant for kinetic modelling of a given metabolic pathway .
LINK eGIFT (Extracting Gene Information From Text) online
LINK InterMine Complex data integration (standalone) .
LINK EnrichNet - Network-based enrichment analysis Enter your gene/protein set of interest online
LINK MyMiner: a web application for computer-assisted biocuration and text annotation .
LINK OLSVis is a visual browser for EBI s OLS (Ontology Lookup Service) : a structured collection of terminology across various biological domains .
LINK top 100 drugs .
LINK Poster: top 200 drugs .
LINK PatientsLikeMe: Share your experiences with treatments. Find patients just like you .
LINK International Clinical Trials Registry Platform (ICTRP) What is a clinical trial? What is trial registration? WHO .
LINK OBRC: Online Bioinformatics Resources Collection .
LINK Trialtrove is the world s most comprehensive real-time source of pharmaceutical clinical trials intelligence, gathering clinical trial information from over 20,000 clinical trial data sources to provide a continually updated reference of clinical trials research in more than 150 countries database
LINK EudraCT is a database of clinical trials in EU database
LINK ClinicalTrials.gov is a registry and results database of publicly and privately supported clinical studies of human participants conducted around the world database
LINK FDA Post-Approval Studies database
LINK UK Biobank is a major national health resource, with the aim of improving the prevention, diagnosis and treatment of a wide range of serious and life-threatening illnesses, including cancer, heart diseases, stroke, diabetes, arthritis, osteoporosis, eye disorders, depression and forms of dementia. UK Biobank recruited 500,000 people aged between 40-69 years in 2006-2010 from across the country to take part in this project. They have undergone measures, provided blood, urine and saliva samples for future analysis, detailed information about themselves and agreed to have their health followed. Over many years this will build into a powerful resource to help scientists discover why some people develop particular diseases and others do not database
LINK Protein level predictions 1 - Pathogenic or not .
LINK Directory of computer-aided Drug Design tools Drug Design tools
LINK Cytochrome P450 interactions training CYP
LINK Resources on bioinformatics classified by categories .
LINK The NCBI BioSystems Database, One type of biosystem is a biological pathway, which can consist of interacting genes, proteins, and small molecules. Another type of biosystem is a disease, which can involve components such as genes, biomarkers, and drugs .
LINK The Human Variome Project is currently working with the World Health Organization (WHO) and other partners on a consultation to determine the feasibility of establishing a global program on human genomics and public health .
LINK The International HapMap Project is a partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom and the United States to develop a public resource that will help researchers find genes associated with human disease and response to pharmaceuticals database
LINK dbSNP short genetic variation database
LINK JSNP: a database of common gene variations in the Japanese population database
LINK 1000Genomes at NCBI .
LINK Pathguide contains information about 325 biological pathway related resources and molecular interaction related resources including Protein-Protein Interactions and many others A pathway resource list
LINK Sixty-Four Free Chemistry (and related) Databases .
LINK PSICQUIC View links to multiple molecular interaction databases .
LINK The Bioinformatics Links Directory features curated links to molecular resources, in silico tools and databases List of tools essentially from NAR issues, tends to focus on bioinformatics, genomics but some tools are for drugs and structural bioinformatics
LINK SCT : French Society for drug discovery .
LINK SFCi : French Society of Chemoinformatics .
LINK WWW computational chemistry resources Chemistry tools
LINK Links to the Theoretical and Computational Biophysics group - list of tools essentially for macromolecules .
LINK The oreChem Project: Integrating Chemistry Scholarship with the Semantic Web. .
LINK Many tools for modeling and mining small molecules, proteins, DNA, RNA, partial charges...solvent accessible molecular surface area with MASKER... .
LINK Numerous info about chemoinformatics chemoinformatics data set, IC50 on several targets
LINK Numerous links for chemistry and computer tools Many chemistry links by Dr. L P Taylor
LINK PolySearch supports more than 50 different classes of queries against nearly a dozen different types of text, scientific abstract or bioinformatic databases online
LINK iHOP: information hyperlinked over proteins online
LINK ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes standalone
LINK Frisbi: FRENCH INFRASTRUCTURE FOR INTEGRATED STRUCTURAL BIOLOGY international project structural biology
LINK IPAD: the Integrated Pathway Analysis Database for Systematic Enrichment Analysis (a new resource for analyzing, identifying, and validating pathway, disease, drug, organ specificity and their inter-associations) database
LINK The barcode algorithm is designed to estimate which genes are expressed in tissues database
LINK FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment database
Open innovation in drug discovery and related projects
LINK The European Lead Factory is a pan-European platform for drug discovery supported by the Innovative Medicines Initiative (IMI) that is set to give a major boost to drug discovery in Europe .
LINK EU-OPENSCREEN, the European Infrastructure of Open Screening Platforms for Chemical Biology .
LINK ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies .
LINK ChemBioNet: A Resource Network Supporting Academic Chemical Biology Research .
LINK Grants4Targets, Grants for Target ID, validation in oncology, gynecology, cardiology, and hematology, Bayer .
LINK MRC Technology, Basic research on therapeutic antibody targets .
LINK Phenotypic Drug Discovery (PD2) Lilly, Screening of external molecules in phenotypic modules to identify compounds of potential therapeutic utility; possible collaboration with compounds of mutual interest .
LINK Screening of external molecules in target-based assays, Lilly .
LINK CTSA portal, Industry and academia collaboration in drug repositioning .
LINK NIH Chemical genomic center (NCGC)-pharmaceutical collection (NPC) .
LINK Pharma in Partnership (PiP) Program, GSK .
LINK European Rare Diseases Therapeutic Initiative (ERDITI) Public-Private .
LINK Rare diseases and orphan drugs .
LINK Screening for rare diseases .
LINK Collaborative Drug Discovery: The CDD public Database enables scientists to archive, mine, and collaborate around pre-clinical chemical and biological drug discovery data through a web-based interface .
LINK Center of Excellence for External Drug Discovery (CEEDD) GSK sponsored; Virtual company .
LINK Biogen Idec Innovation Incubator (Bi3) .


URLs Off-targets, polypharmacology, Adverse drug reactions (ADR), prediction of bioactivity Comments
LINK EU-ADR Web Platform Exploring and Understanding Adverse Drug Reactions By Integrative Mining of Clinical Records and Biomedical Knowledge online, need to register
LINK Data-Driven Prediction of Drug Effects and Interactions: database of drug effects (Offsides) and a database of drug-drug interaction side effects (Twosides) (Altman lab) http://helix-web.stanford.edu/download/tatonetti/3003377s-offsides.zip and http://helix-web.stanford.edu/download/tatonetti/3003377s-twosides.zip, should be also available at PharmGKB datasets
LINK PharmGKB is a knowledge base that captures the relationships between drugs, diseases/phenotypes and genes involved in pharmacokinetics (PK) and pharmacodynamics (PD) ADME/tox; PK/PD, online
LINK The Natural-Product-Likeness scoring system is implemented as Taverna 2.2 workflows, and is available under Creative Commons Attribution-Share Alike 3.0 Unported License at http://www.myexperiment.org/packs/183.html. The present link goes to the executable standalone java package (under Academic Free License) standalone
LINK FINDSITE-COMB (see also FINDSITE-LHM is a homology modeling approach to flexible ligand docking), and Curr Opin Struct Biol. 2013 Feb 14, by Skolnick J et al online
LINK Molinspiration: predict bioactivity, Score a compound for its ability to be GPCR ligand, ion channel modulator, kinase inhibitor, nuclear receptor ligand, protease inhibitor, enzyme inhibitor. Based on Bayesian statistics to compare structures of representative ligands active on the particular target with structures of inactive molecules and to identify substructure features (which in turn determine physicochemical properties) typical for active molecules online
LINK DrugDigest is a noncommercial, evidence-based, consumer health and drug information site dedicated to empowering consumers to make informed choices about drugs and treatment options database
LINK The FDA Adverse Event Reporting System (FAERS) is a database that contains information on adverse event and medication error reports submitted to FDA database
LINK The Metabolism and Transport Drug Interaction Database (DIDB) and the Pharmacogenetics Database (e-PKGene) are part of a knowledge base (DIDB platform) designed for scientists and clinicians working in the field of drug development, drug disposition and drug-drug interactions (DDIs). The DIDB platform was developed at the University of Washington s Department of Pharmaceutics, School of Pharmacy with input from pre-clinical and clinical pharmaceutical scientists. The DIDB was first licensed in 2002 and is currently used by a large number of pharmaceutical companies, regulatory agencies, contract research organizations and academic institutions worldwide database commercial
LINK P450 Drug Interaction Table database
LINK The Clinical Practice Research Datalink (CPRD) is the new English NHS observational data and interventional research service, jointly funded by the NHS National Institute for Health Research (NIHR) and the Medicines and Healthcare products Regulatory Agency (MHRA). CPRD services are designed to maximise the way anonymised NHS clinical data can be linked to enable many types of observational research and deliver research outputs that are beneficial to improving and safeguarding public health database
LINK SuperToxic database database
LINK The Vaccine Adverse Event Reporting System (VAERS) database
LINK VigiBase is a unique collection of international drug safety data. The data is available in a wide range of services, from advanced statistical analysis to basic case report retrieval database, commercial
LINK PharmaTrek, Polypharmacology online
LINK ChemBl online
LINK Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data Polypharmacology, ADR, off-targets, online
LINK FragmentStore : a comprehensive database of fragments linking metabolites, toxic molecules and drugs - database possible off-target interactions, online
LINK SePreSA A drug molecule is submitted to the server and its potential interaction with multiple adverse drug reaction targets is calculated using DOCK program Small molecule docking - admet - off-targets, online
LINK BioDrugScreen: Computational drug design and discovery resource and server. The portal contains the DOPIN (Docked Proteome Interaction Network) database constituted by millions of pre-docked and pre-scored complexes from thousands of targets from the human proteome and thousands of drug-like small molecules from the NCI diversity set and other sources. The portal is also a server that can be used to (i) customize scoring functions and apply them to rank molecules and targets in DOPIN; (ii) dock against pre-processed targets of the PDB; and (iii) search for off-targets online
LINK The ElectroShape Polypharmacology server is a tool that enables any user to estimate polypharmacology profiles and side effects of compounds based on the molecular similarity concept off-target, online
LINK TargetHunter of Small Molecule is designed and constructed to identify possible targets of small molecules by searching the available bioactive compound-target pairs from various resource using the query structure off-target, online
LINK ChemProt2: a disease chemical biology database. Profiling. In Press, NAR, by Taboureau et al. disease chemical biology database off-target, online
LINK PASS Inet 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. off-target, tox...online
LINK The AMBIT web services package is one of the several existing independent implementations of the OpenTox Application Programming Interface and is built according to the principles of the Representational State Transfer (REST) architecture. The Open Source Predictive Toxicology Framework, developed by the partners in the EC FP7 OpenTox project, aims at providing a unified access to toxicity data and predictive models, as well as validation procedures. This is achieved by i) an information model, based on a common OWL-DL ontology ii) links to related ontologies; iii) data and algorithms, available through a standardized REST web services interface, where every compound, data set or predictive method has a unique web address, used to retrieve its Resource Description Framework (RDF) representation, or initiate the associated calculations.The AMBIT web services package has been developed as an extension of AMBIT modules, adding the ability to create (Quantitative) Structure-Activity Relationship (QSAR) models and providing an OpenTox API compliant interface standalone
LINK GUSAR: Quantitative prediction of antitarget interaction profiles for chemical compounds online
LINK STITCH: Chemical-Protein Interactions Chemical-Protein Interactions - off-target, online
LINK TarFisDock : a web server for identifying drug targets with docking approach off-target, online
LINK DRAR-CPI: drug repositioning and adverse drug reaction repositioning and Tox, online
LINK PubChem Promiscuity: a web resource for gathering compound promiscuity data from PubChem drug-repositioning off-target, online
LINK PROMISCUOUS: a database for network-based drug-repositioning drug-repositioning off-target
LINK PharmMapper Server is designed to identify potential target candidates for the given probe small molecules off-target, online
LINK ReverseScreen3D, Profiling off-target, online
LINK Similarity ensemble approach (SEA) off-target, online
LINK SuperDrug database: contains 2.396 compounds Drug Database
LINK PDSP: NIMH Psychoactive Drug Screening Program CNS
LINK DrugBank: Numerous data about drugs and targets including drugs already in use (Wishart et al. 2006, new version in 2011) Drug Database
LINK Drug3k: Prescription drug information for consumers Prescription drug information for consumers
LINK SIDER 2 online
LINK idTarget: a server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach online
LINK e-Drug3D offers a facility to explore FDA approved drugs online


URLs Targets & Target-ligand databases Comments
LINK PTID: an integrated web resource and computational tool for agrochemical discovery online
LINK PLI: a web-based tool for the comparison of protein-ligand interactions observed on PDB structures database
LINK the Common Molecules collection, part of the Reciprocal Net project. The molecules in this site are considered common based on their general use or presence in the world in and around us or by the interest they spark because of their fascinating structural properties and innovative applications database
LINK the AlloSteric Database (ASD), the first online database which provides a central resource for the display, search and analysis of the structure, function and related annotation for allosteric molecules database
LINK The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information database
LINK Discovery-2: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria online
LINK MATADOR is a resource for protein-chemical interactions. It differs from other resources such as DrugBank in its inclusion of as many direct and indirect interactions as we could find. In contrast, DrugBank usually contains only the main mode of interacton. The manually annotated list of direct (binding) and indirect interactions between proteins and chemicals was assembled by automated text-mining followed by manual curation database
LINK canEvolve: A Web Portal for Integrative Oncogenomics online
LINK BioModels Database: repository of computational models in biology online database
LINK The EBI has a developed and maintained a number of protein structure related databases. The Protein Databank in Europe (PDBe) group, within the EBI, is responsible for the deposition and validation of new protein structures online database
LINK Brenda: The Comprehensive Enzyme Information System online database
LINK The Enzyme Portal: A case study in applying user-centred design methods in bioinformatics database
LINK PSMDB : The protein-small-molecule database, a non-redundant structural resource for the analysis of protein-ligand binding database online
LINK EC-PDB database contains the known enzyme structures that have been deposited in the Protein Data Bank (PDB)online database
LINK MDB: Metalloprotein database and browser online database
LINK HMRbase is a manually curated database of Hormones and their Receptorsonline database
LINK SDAP is a Web server that integrates a database of allergenic proteins with various computational tools that can assist structural biology studies related to allergensonline
LINK KChannelDB: A Molecular Specific Information System for Potassium channelsonline database
LINK NucleaRDB : An Information System for Nuclear Receptorsonline database
LINK Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains Annotating Genomes with Structures, many tools
LINK NPIDB: nucleic acid protein interaction database database online
LINK Glycan fragment database: a database of PDB-based glycan 3D structures online database
LINK KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms online database
LINK SeRAPhiC. Dataset of about 50 high-quality protein-fragment complexes datasets
LINK BAPPL complexes set. 161 protein-ligand complexes with experimental and estimated binding free energies datasets
LINK SciClips, ddTargets (drug targets / disease target database) Targets & Small molecules, database
LINK AtlasCBS is a tool that allows you to explore chemico-biological space using Ligand Efficiency Indices (LEIs) as variables navigate in Chemico-Biological Space
LINK CSAR A Resource for Docking and Scoring Development Community Structure-Activity Resource .
LINK MIPS Mammalian Protein-Protein Interaction Database online
LINK The Negatome is a collection of protein and domain pairs which are unlikely engaged in direct physical interactions Macromolecules, database
LINK GPCRDB: GPCR-specific PDF reader .
LINK GPCR SARfari is an integrated chemogenomics workbench focussed on GPCRs GPCR Database
LINK The GDD, a GPCR Decoy Database, with its accompanying GPCR Ligand Library (GLL) have been compiled to help in GPCR docking. C Cavasotto GPCR-ligand Database
LINK kinase.com explores the functions, evolution and diversity of protein kinases, the key controllers of cell behavior Database
LINK GLIDA: GPCR ligand database GPCR-ligand Database
LINK SuperTarget integrates drug-related information, over 6000 targets, 195000 compounds, 282 drug-target pathways...57 CYP Compound Database, Macromolecules
LINK PDSP: the database has 46,134 Ki values for searching, and is growing Compound Database, Macromolecules
LINK Iridium: A Highly Trustworthy Protein-Ligand Structure Database Database, dataset
LINK AutoBind :Automatic extraction of protein–ligand-binding affinity data online
LINK PDBbind: macromolecules with co-crystallized ligands and experimental binding affinities Compound Database, Macromolecules
LINK Scorpio (structure-calorimetry of reported protein interactions online): This is a FREE online repository of protein-ligand complexes which have been structurally resolved and thermodynamically characterised database
LINK KiBank: Proteins with co-crystallized ligands and experimental binding affinities Compound Database, Macromolecules
LINK RELIBASE: Proteins with co-crystallized ligands and CavBase Compound Database, Macromolecules
LINK BioLiP (biologically relevant ligand-protein binding interactions) is a semi-manually curated database for high-quality database
LINK Drug-Target Interactome (DTome) Compound Database, Macromolecules
LINK CCDC/Astex validation test set: 305 protein-ligand complexes to calibrate docking and scoring tools datasets
LINK AffinDB: Proteins with co-crystallized ligands and experimental binding affinities database
LINK UniDrug-target: a computational tool to identify unique drug targets in pathogenic bacteria, compares proteome sequences of pathogenic strain(s) against sequences of nonpathogenic and beneficial strains of bacteria as well as human proteomes to identify pathogen-specific proteins in the former online
LINK LIBP-Pred: web server for lipid binding proteins online
LINK VeryGene: linking tissue-specific genes to diseases, drugs, and beyond for knowledge discovery database
LINK Trypano-PPI: a web server for prediction of unique targets in trypanosome proteome online
LINK SuperPred: drug classification and target prediction online
LINK PDTD: a web-accessible protein database for drug target identification online
LINK KEGG: Kyoto Encyclopedia of Genes and Genomes online database
LINK The Connectivity Map (also known as Cmap) is a collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms that together enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene-expression changes online database
LINK sscMap: Connecting small-molecule drugs using gene-expression signatures standalone
LINK The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence database
LINK GeneBank, DNA sequences database
LINK Gene Expression Omnibus: a public functional genomics data repository database
LINK TDD Therapeutic Target Database online database
LINK Drug-Target Interactome (DTome) Compound Database, Macromolecules
LINK SuperTarget integrates drug-related information Compound Database, Macromolecules
LINK SciClips, ddTargets (drug targets / disease target database) Targets - New targets
LINK TissueDistributionDBs : is a repository of tissue distribution profiles for identifying and ranking the genes in the spectrum of tissue specificity based on Expressed Sequence Tags (ESTs) online
LINK DART (Ji et al. 2003), ADME-AP (Sun et al. 2002), TRMP (Zheng et al. 2004), TTD (Chen et al. 2002a): databases for facilitating the search for drug Absorption, Distribution, Metabolism, Excretion associated proteins. Therapeutic Target Database (268 successful targets in TTD in May 2007) Databases for ADME/tox, Toxicity


URLs QSAR Comments
LINK Datasets in SDF for training and testing software from J Bajorath ligands, training sets
LINK Stereo signature molecular descriptor standalone
LINK WEBCDK: CDK online computation of descriptors, does not seem to work, check somewhere here http://crdd.osdd.net/, no comment yet from the webmaster online
LINK Mold2: Descriptors Generator Software standalone
LINK The 4D Flexible Atom-Pair Kernel represents a 4D similarity measure for molecular graphs (4D FAP) standalone
LINK BioVenn: a web application for the comparison and visualization of biological lists using area proportional Venn diagrams online
LINK BlueDesc - Molecular Descriptor Calculator, A key step in classical quantitative structure-activity/property relationship (QSAR/QSPR) modeling is the encoding of a chemical compound into a vector of numerical descriptors. Although most of the available chemoinformatic software packages provide routines for the calculation of descriptors they are not easy to use in most cases. This simple command-line tool converts an MDL SD file into ARFF and LIBSVM format for machine learning and data mining purposes using CDK and JOELib2. Compounds in 3D standalone
LINK Water solublity (logS) database (several others, logBB, P-gp, Caco-2, oral...) datasets
LINK Large, chemically diverse dataset of logP measurements for benchmarking studies, 707 validated logP values ranging from 0.30 to 7.50, molecules in SMILES, Eur J Pharm Sci. 2013 48 (Martel S, Gillerat F, Carosati E, Maiarelli D, Tetko IV, Mannhold R, Carrupt PA) log P dataset
LINK Emanuele Perola An Analysis of the Binding Efficiencies of Drugs and Their Leads in Successful Drug Discovery Programs J Med Chem 2010, Supporting Info, leads and corresponding drugs in SDF dataset
LINK Strip-it is a tool to extract molecular scaffolds according predefined rules based on definitions as described by Murcko, Pollock and Schuffenhauer standalone resources for QSAR & modeling professionals
LINK QSAR World is a free online resource for QSAR & modeling professionals that provides comprehensive information on technical aspects, makes manually curated datasets available freely and provides listing of many major other resources Free online resource for QSAR, dataset, sever down?
LINK Interpretable correlation descriptors for quantitative structure-activity relationships.The topological maximum cross correlation (TMACC) descriptors are alignment independent 2D descriptors for the derivation of QSARs standalone
LINK Links to cheminformatics programs and QSAR datasets. These include, diversity and similarity searches. Many compounds designed for specific targets (e.g., coagulation factor Xa...), AMES, toxicity.... Many datasets Compound searching - Datasets - Database
LINK A graphical tool for structure-activity studies on Windows. SOMFA is a new technique for 3D QSAR designed by Peter Winn and Daniel Robinson. The method is very simple and avoids statistical selection procedures such as PLS. All tests so far show it to be as good as other QSAR methods, and better than many. The SOMFA code and executable may be downloaded Structure-activity, SOMFA (on Windows only, server down?)
LINK E-DRAGON is the electronic remote version of the well known software DRAGON, which is an application for the calculation of molecular descriptors developed by the Milano Chemometrics and QSAR Research Group of Prof. R. Todeschini. These descriptors can be used to evaluate molecular structure-activity or structure-property relationships, as well as for similarity analysis and highthroughput screening of molecule databases. Compute molecular properties
LINK QSAR training. What is the (Q)SAR Application Toolbox? The Toolbox is a software application intended to be used by governments, chemical industry and other stakeholders in filling gaps in (eco)toxicity data needed for assessing the hazards of chemicals. Chemoinformatics - QSAR
LINK The OCHEM is an online database with modeling environment. Many data sets available, like for ADMET QSAR modeling, you can submit your experimental data, or you use other users' data to build predictive QSAR models for physical-chemical or biological properties (Tetko IV et al), contains ToxAlerts Chemistry tools - toolkit - chemoinformatics - Biostatistics
LINK Software list from the QSAR and Modelling society, datasets information datasets
LINK OECD QSAR Toolbox ADME/tox standalone
LINK open3dqsar: An open-source software aimed at high-throughput chemometric analysis of molecular interaction fields QSAR
LINK McQSAR generates quantitative structure-activity relationships (QSAR equations) using the genetic function approximation paradigm standalone
LINK PaDEL-Descriptor: calculate molecular descriptors and fingerprints. The software currently calculates 863 descriptors (729 1D, 2D descriptors and 134 3D descriptors) and 10 types of fingerprints standalone
LINK SMIREP is a system for predicting the structural activity of chemical compounds standalone
LINK 3-D QSAR MODELS DATABASE for Virtual Screening online tools and datasets
LINK MOLE db. Molecular Descriptors DataBase is a free on-line database comprised of 1124 molecular descriptors calculated for 234773 molecules database online
LINK ChemDB portal: Datasets. Experimentally annotated subsets datasets for some targets including ADMET and also for organs
LINK MolInfo: Calculate descriptors for a Molecule (ChemDB portal) online
LINK Pattern Match Counter. Counts Functional Groups (sub-structures) in molecules online
LINK Partial Least Squares Regression online
LINK MOLFEAT For computing molecular fingerprints and molecular descriptors of molecules from their 3D structures, and for computing activity of compounds of specific chemical types against selected targets based on published Quantitative Structure-Activity Relationship (QSAR) models online