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 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
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