Binding pockets & pocket-ligand datasets

Binding pockets: prediction & comparison

  • SIENA - Efficient Compilation of Selective Protein Binding Site Ensembles (2016) - online
  • DeepSite - Binding pocket predictor, neural networks (2017) - online
  • bSiteFinder - Web server for indentifying protein-binding sites (2016) - online
  • IsoMIF - The IsoMIF Finder Interface allows you to identify binding site molecular interaction field (MIF) similarities between a query protein structure and a database of pre-calculated MIFs or user defined cavity MIFs (2016) - online
  • canSAR - An updated cancer research and drug discovery knowledgebase (2016) - online
  • ISMBLab-LIG - The ISMBLab-LIG algorithm has substantial tolerance to the prediction uncertainties of computationally derived protein structure models - online
  • AFAL - A web service for profiling amino acids surrounding ligands in proteins (not working in May 2016, to check) - online
  • BindUP - A web server for non-homology-based prediction of DNA and RNA binding proteins. Gene expression is a multi-step process involving many layers of regulation. The main regulators of the pathway are DNA and RNA binding proteins (2016) - online
  • MANORAA - Mapping Analogous Nuclei Onto Residue And Affinity for identifying protein–ligand fragment interaction, pathways and SNPs - online
  • AutoSite - an automated approach for pseudo-ligands prediction-from ligand-binding sites identification to predicting key ligand atoms (2016) - standalone
  • EDTSurf - Pocket, surface, pocket depth...etc - standalone
  • DrugFEATURE - Identifying Druggable Targets by Protein Microenvironments Matching: Application to Transcription Factors (2014) - standalone
  • DruGUI - DruGUI is a VMD plugin designed for setup and analysis of simulations containing small organic molecules (probes) for druggability assessment. DruGUI can incorporate a diverse set of molecules from CHARMM General Force Field (CGenFF) into simulations - standalone
  • KVFinder - Find binding pockets - standalone
  • PCS - Protein cavity search - standalone
  • TM-align - Algorithm for sequence-order independent protein structure comparisons - online
  • RBscore - RNA binding score is a web server to predict RNA/DNA binding sites on protein - online
  • fPOP - Footprinting protein functional surfaces by comparative spatial patterns - online
  • CryptoSite - Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites (2016) - online
  • SPRINT - Sequence-based prediction of protein-peptide binding sites using support vector machine (2016) - online
  • AllosMod - Modeling of Ligand-induced Protein Dynamics and Beyond - online
  • DrugMiner - The DrugMiner web tool was developed based on the findings of this study to provide researchers with the ability to predict druggable proteins (2016) - online
  • ASDB - Annotated Scaffold Database, a computer-readable and systematic target-annotated scaffold database (2016) - online
  • PLIP - Fully automated protein–ligand interaction profiler (2015) - online
  • AlloPred - Prediction of allosteric pockets on proteins using normal mode perturbation analysis (2015) - online
  • ProBiS-CHARMMing - Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites (2015) - online
  • CHEXVIS - A tool for molecular channel extraction and visualization (2015) - online
  • IsoMIF - Detection of Binding Site Molecular Interaction Field Similarities (2015) - online and standalone
  • Phyre2 - The server (version 2015) which uses advanced remote homology detection methods to build 3D models (homology modeling - comparative modeling) predicts also ligand binding sites and analyze the effect of amino acid variants (e.g., nonsynonymous SNPs (nsSNPs)) starting with a user's protein sequence - online
  • PatternQuery - Server for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank - online
  • PocketOptimizer - Prediction of affinity increasing mutations in a protein-binding pocket - standalone
  • JEDI - The fast, continuous and differentiable JEDI druggability estimator has been implemented in PLUMED. JEDI (Just Exploring Druggability at protein Interfaces), features a druggability potential made of a combination of empirical descriptors that can be collected “on-the-fly” during MD simulations (2015) - standalone
  • tconcoord - Generate pocket ensemble - pocket flexibility - standalone
  • AlphaSpace - Fragment-Centric Topographical Mapping to Target Protein-Protein Interaction Interfaces (2015) - standalone
  • ASCONA - Rapid Detection and Alignment of Protein Binding Site Conformations (2015) - standalone
  • WATCLUST - A tool for improving the design of drugs based on protein-water interactions. The tool also allows direct transfer of the WS information to Autodock program to perform biased docking (VMD plugin) - standalone
  • Descriptors - PCI: Pocket Convexity Index. Pocket Sphericity Index - standalone
  • Link - BetaCavityWeb: A server for molecular voids and channels - online
  • Epock - Rapid analysis of protein pocket dynamics (2014-2015) - standalone
  • BetaMol - A molecular modeling, visualization, and analysis program, check pockets - standalone, windows
  • BetaConcept - BetaConcept program from VDRC to explore the properties of the beta-shape. Pocket visualization and prediction (2015). Optimal Ligand Descriptor for Pocket Recognition Based on the Beta-Shape - standalone, windows
  • CCD - The Chemical Component Dictionary is a chemical reference data resource that describes all residue and small molecule components found in Protein Data Bank (PDB) entries - datasets
  • ASBench - Benchmarking sets for allosteric drug discovery - datasets
  • LigDig - A web server for querying ligand–protein interactions - online
  • Pocket-tool - MSPocket: an orientation-independent algorithm for the detection of ligand binding pockets - standalone
  • Cavity_align - Align pockets - online
  • SplitPocket - Pocket tool - online
  • Link - protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences ProtrWeb, a user-friendly web server for calculating descriptors presented in the protr package (2015) - online
  • SPACER - Analyzes protein structure, finds potential functional/effector binding sites, and shows allosteric communication between the sites - online
  • MODA - Membrane optimal docking area. A tool to predict online potential membrane binding site on a protein 3D structure - online
  • Platinum - A database of experimentally measured effects of mutations on structurally defined protein-ligand complexes (around 1000 mutations in 2014) - database
  • Het-PDB Navi - A database for protein-small molecule interactions - database
  • POVME - An Enhanced Tool for Determining Pocket Shape and Volume Characteristics - standalone
  • PockDrug - A model for predicting pocket druggability that overcomes pocket estimation uncertainties - online
  • Polyphony - Superposition independent methods for ensemble-based drug discovery. Currently, methods capable of the analysis of ensembles of crystal structures and MD trajectories are limited and usually rely upon least squares superposition of coordinates. New methodologies are described and validated for the superimposition independent conformational analysis of large collections of structures or simulation snapshots of the same protein. The methodologies are encoded in a Python package - standalone
  • Link - MotiveValidator: Interactive web-based validation of ligand and residue structure in biomolecular complexes. MotiveValidator can be used for testing single structures, or the analysis of large sets of ligands or fragments prepared for binding site analysis, docking or virtual screening - online
  • eMatchSite - Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models - Online
  • PeptiSite - A structural database of peptide binding sites in 4D - database
  • iDrug - A web-accessible and interactive drug discovery and design platform. Computer-aided drug design based on pharmacophore and 3D molecular similarity searching. The web interface enables binding sites detection, virtual screening hits identification, and drug targets prediction in an interactive manner through a seamless interface to all adapted packages (e.g., Cavity, PocketV.2, PharmMapper, SHAFTS). Several commercially available compound databases for hit identification and a well-annotated pharmacophore database for drug targets prediction were integrated in iDrug as well. The web interface provides tools for real-time molecular building/editing, converting, displaying, and analyzing - online
  • CHED - This site uses the 'CHED' algorithm to predict 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
  • RBPmap - A web server for mapping binding sites of RNA-binding proteins - online
  • pocketZebra - A web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families - online
  • ProBiS - ProBIS-ligands: A web server for prediction of ligands by examination of protein binding sites - online
  • GalaxySite - GalaxySite: ligand-binding-site prediction by using molecular docking (GalaxyWeb) - online
  • CAD-score - The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes - online
  • SMAP - SMAP software package is designed for the comparison and the similarity search of protein three-dimensional motifs independent on the sequence order - online
  • RASMOT - RASMOT-3D PRO searches in protein structure files for proteins possessing a group of residues in a topology similar to that adopted by a 3D motif given in input - online
  • eF-surf - Molecular surface of proteins with the electrostatic potential is a representation of protein three dimensional structures, which often gives some clues to infer the function of proteins - online
  • FunClust - FunClust is a web server for the identification of local functional motifs in a set of non homologous protein structures. You can submit a set of protein structures deemed to share a common function (e. g. they bind similar ligands, interact with similar protein interfaces or share an enzymatic activity) - online
  • Rosetta - RosettaBackrub: Flexible backbone protein structure modeling and design server. Can be used for Point mutation, Backbone ensemble (creates near-native structural ensembles), Sequence tolerance (predicts sequences tolerated for proteins and protein-protein interfaces using flexible backbone design methods. Example applications are the generation of sequence libraries for experimental screening and prediction of protein or peptide interaction specificity) - online
  • MolSite - A ligand-binding site prediction. MolSite predicts ligand-binding site of target protein and its affinity by a compound docking simulation - Ask the authors, standalone
  • TuberQ - Shows the potential Druggability, using both structural and biological related aspects, for each of the proteins of the Mycobacterium tuberculosis (Mt) genome - online
  • LigandRFs - Predict ligand-binding sites from sequence information through random forests - standalone
  • 3D-SURFER - a web-based platform for rapid protein surface analysis and comparison. 3D-SURFER integrates global surface shape similarity-based search using 3D Zernike Descriptors, and local structure analysis using VisGrid and LIGSITEcsc - online
  • PSC - Protein surface classification - online
  • APROPOS - Geometry-based pocket prediction - standalone
  • pvSOAR - pvSOAR takes a PDB ID or structure file as input, and searches for other proteins with surface regions that are similar to the query structure. May not work anymore - online
  • GIRAF - Fast search and flexible alignment of ligand binding interfaces - standalone
  • IMAAAGINE - Search a hypothetical 3D protein arrangement in the Protein Data Bank (can find a pocket or region similar to a query) - online
  • Phosfinder - Predicts phosphate binding sites - online
  • Nucleos - Predicts nucleotide-binding sites - online
  • CatSId - Search for matches between catalytic sites and proteins (compare binding site) - online
  • COFACTOR - COFACTOR is a structure-based method for biological function annotation of protein molecules. To use COFACTOR, user needs to provide a 3D-structural model of the protein of interest. COFACTOR will thread the structure through the BioLiP protein funtion database by local and global structure matches to identify functional sites and homologies. Functional insights, including ligand-binding site, gene-ontology terms, and enzyme classification, will be derived from the best functional homology template - online
  • STP - Surface triplet propensities: Identification of protein binding surfaces using surface triplet propensities. The method described here does not explicitly look for cavities but uses small surface patches consisting of triplets of adjacent surface atomic groups that can be touched simultaneously by a probe sphere representing a solvent molecule - online
  • LigPlot - The program LigPlot to look at protein-ligand interaction is available online via the PDBsum Web pages - online
  • PARS - PARS: a web server for the prediction of Protein Allosteric and Regulatory Sites - online
  • COACH - A meta-server approach to protein-ligand binding site prediction - online
  • BSR - 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
  • Firestar - Predictions of functionally important residues using the large inventory of functionally important residues in the FireDB database - online
  • CNIO - Combines predictions from Firestar and 3DLigandSite - online
  • CAMEO - Continuously evaluate the accuracy and reliability of predictions (protein and binding site) - .
  • DB - NeutralMUTDB: Neutral Binding-site Mutation Dataset - database
  • IsoCleft - IsoCleft Finder is a web-based tool for the detection of local structural and chemical similarities between potential smallmolecule binding cavities and a non-redundant dataset of known small-molecule binding-sites. The dataset, available for download, is composed of 7339 entries representing unique Pfam PDB-ligand (hetero group code) combinations with known levels of cognateligand similarity - online
  • cGRILL - A simple affinity map generator. cGRILL calculates 4 affinity maps: lipophilic (CH3), hydrogen bond acceptor (=O), hydrogen bond donor (NH4+) and mixed hydrogen bond donor-acceptor (OH). It implements AMBER force field van der Waals and electrostatic terms and a custom hydrogen bond - standalone
  • Ligbase - A Structural Database of Aligned Ligand Binding Sites - Ligbase - database
  • metaDBSite - A meta web server for protein DNA-binding sites prediction based on protein sequence - online
  • Drosteppy - identification and analysis of conserved pockets on protein surfaces - online
  • AlloSite - Find allosteric binding site - online
  • PDB_redo - PDB_redo: databank of updated and optimised X-ray structure models, important to check binding pockets and ligands - standalone and online
  • CATHEDRAL - Can align multiple structures without human intervention and could help looking at pockets - online
  • Coot - For macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data. Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots, skeletonization, non crystallographic symmetry and more. Can be used to analyze ligand-binding pocket - standalone
  • Twilight - Visualizing Ligand Molecules in Twilight Electron Density (quality control, Xray ligand) - standalone
  • RaptorX - Protein structure prediction program, Given an input sequence, RaptorX predicts its secondary and tertiary structures as well as solvent accessibility and disordered regions. RaptorX also assigns the following confidence scores to indicate the quality of a predicted 3D model. got very good results at CASP9 for instance - online
  • VHELIBS - Open source software that aims to ease the validation of binding site and ligand coordinates for non crystallographers. Using a convenient graphical user interface, it allows one to check how ligand and binding site coordinates fit to the electron density map. VHELIBS can use models from either the PDB or the PDB_REDO databank of re-refined and re-built crystallographic models. The user can specify threshold values for a series of properties related to the fit of coordinates to electron density (Real Space R, Real Space Correlation Coefficient and average occupancy are used by default). VHELIBS will automatically classify residues and ligands as Good, Dubious or Bad based on the specified limits. The user is also able to visually check the quality of the fit of residues and ligands to the electron density map and reclassify them if needed - standalone
  • ProACT - Software for the anlysis of protein accessibilities, cavities and contacts and structural/buried water molecules. - standalone
  • Provar - Ensemble analysis of pocket predictions from PASS, LIGSITE, fpocket, SiteMap, CASTp etc. - standalone
  • SimG - An alignment based method for evaluating the similarity of small molecules and binding sites - standalone
  • EPOS_BP - Ensemble of Pockets on Protein Surfaces with BALLPass (EPOSBP) - standalone
  • DR_bind - A server for predicting DNA-binding residues from the protein structure based on electrostatics, evolution and geometry - online
  • eFindSite - Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands - online and standalone
  • FTSite - High accuracy detection of ligand binding sites on unbound protein structures, using small probes. Can work with allosteric sites - online
  • FINDSITE - 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
  • dPred - A program to calculate the desolvation penalties of small probes in cavities to identify possible binding sites of small ligands - standalone
  • AutoMatch - Target-binding protein design and enzyme design by automatic pinpointing potential active sites in available protein scaffolds - standalone
  • FunFOLD - The FunFOLD Binding Site Residue Prediction Server: predicts likely ligand binding site residues for a submitted amino acid sequence - online
  • APoc - Large scale identification of similar protein pockets - software is freely available to ALL users, compare pockets
  • TRAPP - A Tool for Analysis of Transient Binding Pockets in Proteins - online
  • LISE - Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles - online
  • PESDserv - Compares binding sites of proteins - online
  • PocketAlign - Comparison of binding sites - online
  • POOL - Machine learning application for functional site prediction in proteins - online
  • 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
  • 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
  • SOAK - Metal ion binding sites, affinities, and specificity from structure - online
  • PLATINUM - 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
  • PINUP - Protein binding site prediction with an empirical scoring function - online
  • 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
  • DSV - Druggable Site Visualizer is used within Visual Molecular Dynamics (VMD) to inspect and analyze interaction hot spots from FTMap and SiteMap on receptor configurational ensembles - standalone
  • FTMap - Computational solvent mapping is a powerful tool to understand interactions between proteins and solvent molecules. FTMap docks 16 small organic probes on a protein surface (Fast Fourier Transforms), 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. Identifying binding hot spots; determining druggability; providing information for fragment-based drug discovery. Input: protein, DNA or RNA structure, or structure file in PDB format - online
  • FTMap-Param - Same as FTMap, plus determining the low-energy binding poses of up to 15 user-selected probe molecules in hot spot regions. Input: PDB ID of a protein, DNA or RNA structure, or a structure file in PDB format; plus formal charges and SMILES strings to define additional probes - online
  • FTDyn - Mapping potentially large ensembles of protein structures; determining probe-protein interactions for each structure, and averages over the ensemble; identifying the structure most similar to a ligand-bound conformation. Input: Ensemble of protein structures specified in PDB model record format - online
  • FTSite - Identifying likely ligand-binding sites; ranking of sites in terms of probe-protein interactions; listing of binding site residues. Input: PDB ID of a protein structure, protein structure file in PDB format, or a zip file containing up to 15 protein PDB files - online
  • FTFlex - Identifying binding hot spots of proteins and determining druggability, while accounting for side-chain flexibility around selected hot spots; opening pockets in protein-protein interfaces. Stage 1: PDB ID of a protein structure, or protein structure file in PDB format. Stage 2: selection of hot spots for side-chain adjustment and remapping - online
  • FTProd - Binding site comparison across multiple structures - standalone
  • SiMMap - For inferring site-moiety map to recognize interaction preferences between protein pockets and compound moieties - 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
  • aCSM - Noise-free graph-based signatures to large-scale receptor-based ligand prediction. it seems the Link provided by the authors does not work, thus contact directly, paper in Bioinformatics 2013, Pires DE et al - standalone
  • Pocket V2 - A method for deducing receptor-based pharmacophore - standalone
  • AutoMap - A tool for analyzing protein-ligand recognition using multiple ligand binding modes - standalone
  • EzyPred - A top-down approach for predicting enzyme functional classes and sub-classes - online
  • EnzClassPred - EnzClassPred at Bio-AIMS: Enzyme Class Prediction - online
  • AADS - Active Site Prediction of Protein server computes the cavities in a given protein - online
  • Fpocket - Find pocket - geometry-based - standalone
  • FireDB - A database of functionally important residues from proteins of known structure. In addition to the manual curation of ligands, FireDB also provides insights into the biological relevance of individual binding sites - database
  • DrugEBIlity - Structure-based DrugEBIlity: Users can survey different types of druggability scores of a given protein structure - online
  • IFP - Interaction fingerprint, Generates interaction fingerprint for a protein/ligand complex - online
  • 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
  • SiteAlign - Align and compare druggable protein sites - online
  • 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
  • Ghecom - A program for finding multi-scale pockets on protein surfaces using mathematical morphology - online
  • LigSite - LigSite csc: find pockets - online
  • SCREEN2 - Find pockets and gives descriptors - online
  • FunFOLDQA - Pockets - standalone
  • StrucTools - StrucTools is a set of tools commonly used for structural biology calculations with PDB files - online
  • 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
  • Rate4Site - Detects conserved amino-acid sites by computing the relative evolutionary rate for each site in the multiple sequence alignment - standalone
  • PASS - Find pockets - standalone
  • Voidoo - Detection of cavities - standalone
  • SurfNet - Calculation of clefts in protein surfaces - standalone
  • ProBiS - Pocket detection & comparison - online
  • CADDSuite - CADDSuite: A flexible and open framework and workflow system for computer-aided drug design, can find pockets, distant off-target - Ask the authors, standalone
  • McVol - Compute the Volume of Proteins and finding internal cavities - standalone
  • EPOS_BP - Ensemble of Pockets on Protein Surfaces with BALLPass (PASS algorithm was re-implemented) - standalone
  • PoSSuM - 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
  • MANTRA - Mode of Action by NeTwoRk Analysis 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
  • DvD - An R and Cytoscape plug-in for comparing Drug and Disease profiles - standalone
  • FINDSITEcomb - A threading/structure-based, proteomic-scale virtual ligand screening approach - online
  • SiteHound - 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
  • Qhull - Computes the convex hull, Delaunay triangulation... - standalone
  • CASTp - Binding sites and active sites of proteins and DNAs - online and standalone
  • PRIDE - Calculates the PRobability of IDEntity between three-dimensional domains (or whole structures) and offer varied various compararisons with known structures - online
  • 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. Can provide statistics about the type and frequency of residues surrounding different ligands in PDB structures - online
  • PDBeMotif - Motifs and binding Sites, other URL - online
  • MolAxis - Efficient and Accurate Identification of Channels in Macromolecules - online
  • HOLE - Identification of Channels in Macromolecules - standalone
  • 3V - 3V (Voss volume voxelator): Web tool for volume calculation (tunnel and channel - online
  • PoreWalker - PoreWalker is a fully automated method designed to detect and characterize transmembrane protein channels from their 3D structure - online
  • MemSat-SVM - Detecting pore-lining regions in transmembrane protein sequences - standalone
  • CHUNNEL - Travel Distance Code 3.0: Contains Travel Depth, CHUNNEL, CLIPPERS, Burial Depth. CHUNNEL to automatically find, characterize, and display tunnels or pores in proteins - standalone
  • MOLE - A Voronoi Diagram-Based Explorer of Molecular Channels, Pores, and Tunnels - standalone
  • MOLEonline - The Mole package online - online
  • CAVER - A software tool for analysis and visualisation of channels (tunnels) in protein structures - online and standalone
  • PocketDepth - Find pockets - online
  • Erebus - Identifying the location of binding sites on proteins - online
  • 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
  • AutoLigand - Can find binding pockets - standalone
  • Link - Superimpose is a framework for superposition - from protein structure alignment to in silico screening - online
  • Link - PROtein SURFace ExploreR - online
  • 3DLigandSite - Prediction of ligand binding sites, Users can either submit a sequence or a protein structure - online
  • Pocket tool - PocketAnnotate: Functional annotation of proteins - online
  • PocketQuery - Web service for interactively exploring hot regions - online
  • PASS - PASS - online
  • Link - Active Site Prediction of Protein - online
  • SiteComp - Provides 3 major types of binding site analysis (binding site comparison, binding site decomposition to check protein-ligand interaction and guide mutagenesis for instance, and multi-probe characterization) - online
  • ConCavity - ConCavity - online and standalone
  • MOLEonline - MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels - online
  • Cavitor - Find pockets - standalone
  • PocketPicker - Available as a Pymol plugin - standalone
  • 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
  • DMS - Computes molecular surface - open source program written in C, standalone
  • MSMS - Molecular surface and others - standalone
  • GETAREA - GETAREA 1.1: Solvent Accessible Surface Areas - online
  • Pocasa - POcket-CAvity Search Application - online
  • POVME - Measure binding-pocket volumes - standalone
  • 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
  • eF-seek - Protein binding site comparison - online
  • eF-site - Electrostatic surface of functional site - online
  • MetaPocket - Combines 8 pocket methods - online
  • DoGSite - DOGSiteScorer: Binding site prediction, druggability assessment - online
  • SuperStar - Tool for analysis of binding sites - standalone
  • SiteEngines - Functional Sites Structural Search, recognizes regions on the surface of one protein that resemble a specific binding site of another - online
  • PDBSiteScan - Automatically performs the best superposition of sites - online
  • PINTS - Finds reoccuring three-dimensional patterns of amino acids - online
  • Multibind - Multiple Alignment of Protein Binding Sites - online
  • PESDserv - Compare binding sites of proteins - online
  • SUMO - Tools for the analysis of binding sites and to find similar motifs - online
  • RNABindR - RNABindR v2.0: analyzes and predicts RNA-binding sites in proteins - online
  • PAR-3D - Predicts protein active site residues - online
  • PDTD - A web-accessible protein database for drug target identification - database
  • BioDrug - BioDrugScreen - database
  • 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 - database
  • DRAR-CPI - Drug repositioning and adverse drug reaction. about 385 binding pocket, online - database
  • 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) - database
  • Sc-PDB - Tool for analysis of binding sites, database of about 10000 binding pockets - online binding pockets and standalone
  • Pdbfun - Identification of local structural similarities - online
  • SimDOCK - Ligand transposition server - online
  • ProFunc - The ProFunc server help identify the biochemical function of a protein - online
  • eF-Site - eF-Site Electrostatic surface of functional sites - online
  • proSAT2 - Features for visualizing SwissProt and PROSITE functional annotations - online
  • Map3D - FeatureMap3D: Map protein features such as post-translational modifications, protease cleavage sites or exonic structure onto 3D structures of homologous proteins - online
  • ProKware - Integrated system containing interactive graphic interface and abundant protein property annotations a the structural level - online
  • Protemot - Server that carries out prediction of protein binding sites - online
  • KBDOCK - KBDOCK is a 3D database system that defines and spatially clusters protein binding sites for knowledge-based protein docking - online
  • DEPTH - A web server to compute depth and predict small-molecule binding cavities in proteins and predict the pKa of ionizable residues in proteins - online
  • POOL - Server: machine learning application for functional site prediction in proteins - online
  • CrystalDock - Computer algorithm that aids the computational identification of molecular fragments predicted to bind a receptor pocket of interest - standalone
  • Pepsite2 - Prediction of peptide binding sites on protein surfaces - online
  • MCPath - Monte Carlo path generation approach to predict likely allosteric pathways and functional residues - online
  • Link - Catalytic site identification: a web server to identify catalytic site structural matches throughout PDB web server provides the innovative capability to find structural matches to a user-specified catalytic site among all Protein Data Bank proteins rapidly (in less than a minute) - online
  • SPACER - The server provides an interactive framework for exploring allosteric communication in proteins with different sizes, degrees of oligomerization and function - online
  • Nucleos - A web server for the identification of nucleotide-binding sites in protein structures - online
  • LISE - A server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites - online
  • FunFOLD2 - Prediction of protein-ligand interactions - online
  • Adepth - New representation and its implications for atomic depths of macromolecules - online
  • webPDBinder - A server for the identification of ligand binding sites on protein structures - online
  • RBPmotif - A web server for the discovery of sequence and structure preferences of RNA-binding proteins - online
  • PhyloFacts - The PhyloFacts web server: ortholog identification and function prediction using fast approximate tree classification - online
  • PiDNA - Predicting protein-DNA interactions with structural models - online
  • Link - PhysBinder: improving the prediction of transcription factor binding sites by flexible inclusion of biophysical properties - online
  • P.A.R.I.S - Pocket Alignment in Relation to Identification of Substrates - standalone

 

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 - database
  • DCD - Binding pocket database to validate packages predicting druggability - database
  • PSCDB - A database for protein structural change upon ligand binding - database
  • Link - Apo and holo protein dataset - database
  • Pocketome - 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
  • PDBSite - A database on protein active sites and their spatial environment - database
  • CSA - The Catalytic Site Atlas is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure (previously PROCAT) - database
  • SuperSite - The SuperSite is an encyclopedia that is dedicated to a ligand and binding site oriented view of the protein structural space - database
  • NEUTRAL - NeutralmutDB: Neutral Binding-site Mutation Dataset - database
  • PLI - Protein-ligand interaction: It is a database that describes the interactions that a small molecules (identified by a Het_Id code) perform with target proteins, as observed in PDB complexes - database
  • CREDO - CREDO is a relational database storing all pairwise atomic interactions of inter- as well as intra-molecular contacts between small- and macromolecules found in experimentally-determined structures from the Protein Data Bank (PDB) Structural variations from EnsEMBL Variation are mapped onto all protein structures in CREDO through the sequence-to-structure mapping. EnsEMBL Variation contains variation data from the most important sources, including dbSNP, COSMIC and UniProt as well as information about (disease) phenotypes that can be Linked to variations occurring in protein structures. This means that phenotypes can be Linked directly to ligand binding sites or protein-protein interfaces. Interactions between atoms are stored as Structural Interaction Fingerprints (SIFts) that were described first by Deng et al.. CREDO currently implements 13 different interaction types such as hydrogen bonds, halogen bonds, carbonyl interactions and others - database
  • Bival-bind - The Bival-Bind database provides a relatively complete list - 2073 protein complexes with less than 90% sequence identity - out of the protein database, which can serve as bi- or multivalent receptors. Steric clashes of molecular spacers - necessary to connect the monomeric ligand units - with the receptor surface can diminish binding affinity dramatically and, thus, abolish the expected enhancement of binding affinity due to the multivalency. The potential multivalent receptors in the Bival-Bind database are characterized with respect to the receptor surface topography. A height profile between the receptor binding pockets is provided, which is an important information to estimate the influence of unfavorable spacer receptor interaction - database
  • LigandBox - LigandBox (LIGANDs Data Base Open and eXtensible) is a ready-to-dock database of small chemical compounds, for virtual drug screening on computer docking studies. It contains the 3D molecular structures including full hydrogen atoms with atomic charges for each compounds. The KEGG DRUG database has Links to LigandBox. It can search by generic/trade names of a compound, such as tamiflu - database
  • PSMDB - The protein-small-molecule database, a non-redundant structural resource for the analysis of protein-ligand binding. You can find for instance a Non-redundant set of 6733 structures (check the CPLX_25_0.85_7HA.list) - database
  • metaPocket - Benchmark data-sets used in metaPocket 2.0 including a 198 prescription drug-target dataset (found by combining DrugPort and DrugBank search) - database
  • LPDB - Ligand-Protein DataBase - database
  • BioLiP - BioLiP is a semi-manually curated database for high-quality, biologically relevant ligand-protein binding interactions - database
  • DrugPort - Structures of drugs and their target proteins in the PDB - database
  • S3DB - A database of manually curated target and ligand structures, inspired by the Ligand-Protein Database - database
  • PDBbind - The PDBbind core set (version 2013), consists of 195 protein-ligand complexes in 65 clusters with binding constants spanning nearly 10 orders of magnitude. In this data set, 82% ligand molecules are drug-like and 78% protein molecules are validated or potential drug targets - database
  • PocketAnnotate - Non-Redundant Binding Site Database, can compare pockets with PocketMatch - database
  • Last updated on .

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