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Pocket identification software tools | Drug discovery

The prediction of functional sites including ligand binding sites or catalytic sites can guide the design of small molecules that could interact with a protein and modulate its function or drive the selection of targeted mutations for protein…
PickPocket
Web
Desktop

PickPocket

Extrapolates from variants with known binding specificity to those where no…

Extrapolates from variants with known binding specificity to those where no experimental data are available. PickPocket uses information derived from similar protein structures to infer which…

AutoSite
Desktop

AutoSite

An efficient software tool for identifying ligand binding-sites and predicting…

An efficient software tool for identifying ligand binding-sites and predicting pseudo ligand corresponding to each binding site identified. AutoSite identifies ligand-binding sites with higher…

fPOP
Dataset

fPOP footprinting Pockets Of Proteins

Footprinting protein functional surfaces by comparative spatial patterns. fPOP…

Footprinting protein functional surfaces by comparative spatial patterns. fPOP provides the spatial patterns of protein binding sites including both holo and apo forms from more than 40,000…

hpocket
Web

hpocket

A part of a web server, dedicated to centralize information on how to run…

A part of a web server, dedicated to centralize information on how to run fpocket-based online server tools. Hpocket is the application of the pocket tracking approach to collections of homologous…

PocketAnnotate
Web

PocketAnnotate

A computational pipeline for functional annotation of proteins at the level of…

A computational pipeline for functional annotation of proteins at the level of binding sites. PocketAnnotate integrates three in-house algorithms for site-based function annotation: (i) PocketDepth,…

SiMMap
Web

SiMMap Site-Moiety-Map

Provides analysis of Site-Moiety Map. The SiMMap server statistically derives…

Provides analysis of Site-Moiety Map. The SiMMap server statistically derives site-moiety map with several anchors, which describe the relationship between the moiety preferences and physico-chemical…

PockDrug
Web

PockDrug

Predicts pocket druggability, efficient on both; estimated pockets guided by…

Predicts pocket druggability, efficient on both; estimated pockets guided by the ligand proximity (extracted by proximity to a ligand from a holo protein structure using several thresholds) and…

bSiteFinder
Web

bSiteFinder

Identifies protein-binding sites. bSiteFinder algorithm underutilize the…

Identifies protein-binding sites. bSiteFinder algorithm underutilize the increasing numbers of three-dimensional protein–ligand complex structures (bound protein), and could be improved on the…

CryptoSite
Web

CryptoSite

A computational tool for predicting the location of cryptic binding sites in…

A computational tool for predicting the location of cryptic binding sites in proteins and protein complexes. CryptoSite accurately localizes over 96% of cryptic binding sites, outperforming other…

CASTp
Web

CASTp

An online tool that locates and measures pockets and voids on 3D protein…

An online tool that locates and measures pockets and voids on 3D protein structures. CASTp includes annotated functional information of specific residues on the protein structure. The annotations are…

pocketZebra
Web

pocketZebra

Web-server for selection and classification of subfamily-specific binding sites…

Web-server for selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families.

DeepSite
Web

DeepSite

Employs state-of-the-art convolutional neural networks. DeepSite is a pure…

Employs state-of-the-art convolutional neural networks. DeepSite is a pure machine-learning approach developed to predict protein-ligand binding sites. Users can submit jobs to the GPUequipped…

ProteinsPlus
Web

ProteinsPlus

Allows to access and preprocess structural data for all kinds of life science…

Allows to access and preprocess structural data for all kinds of life science research, and gives an immediate visual impression of the overall protein structure and contained ligand molecules. By…

TRAPP webserver
Web

TRAPP webserver

Studies the dynamics of a known binding pocket or any other protein cavity of…

Studies the dynamics of a known binding pocket or any other protein cavity of interest, identifies and characterises transient sub-pockets. TRAPP webserver is an online method to provide the user…

LIBRA
Desktop

LIBRA LIgand Binding site Recognition Application

A software tool that, given a protein’s structural model, predicts the…

A software tool that, given a protein’s structural model, predicts the presence and identity of active sites and/or ligand binding sites. The algorithm implemented by LIBRA is based on a graph…

Epock
Desktop

Epock

An efficient command-line tool that calculates pocket volumes from Molecular…

An efficient command-line tool that calculates pocket volumes from Molecular Dynamics (MD) trajectories. A plugin for the VMD program provides a graphical user interface to facilitate input creation,…

LISE
Web
Desktop

LISE Ligand Interacting Site Enriched

Predicts protein’s ligand-binding sites. LISE is a LBSP method derived from…

Predicts protein’s ligand-binding sites. LISE is a LBSP method derived from 3D motifs of protein–ligand interactions that achieves significantly better success rates, especially in predicting the…

AADS
Web

AADS automated active site detection, docking, and scoring

Computes the cavities in a given protein. AADS is a robust automated active…

Computes the cavities in a given protein. AADS is a robust automated active site detection, docking, and scoring protocol for proteins with known structures. It detects ten cavity points in a protein…

eF-seek
Web

eF-seek

A web server to search for the similar ligand binding sites for the uploaded…

A web server to search for the similar ligand binding sites for the uploaded coordinate file with PDB format. The representative binding sites in eF-site database are search by our own algorithm…

SplitPocket
Web

SplitPocket

A web server to identify functional surfaces of protein from structure…

A web server to identify functional surfaces of protein from structure coordinates.

SITEHOUND
Web

SITEHOUND

Identifies ligand binding sites by computing interactions between a chemical…

Identifies ligand binding sites by computing interactions between a chemical probe and a protein structure.

IonCom
Web
Desktop

IonCom

Implements a ligand-specific method for small ligand (including metal and acid…

Implements a ligand-specific method for small ligand (including metal and acid radical ions) binding site prediction. Starting from given sequences or structures of the query proteins, IonCom…

CCCPP
Desktop

CCCPP Computes Cavities, Channels, Pores and Pockets in proteins

Computes the void parts of the proteins, i.e. cavities, channels and pockets.…

Computes the void parts of the proteins, i.e. cavities, channels and pockets. The present approach is a variant of the alpha shapes method, with the advantage of taking into account the size and the…

fpocket
Web

fpocket

An open source protein pocket (cavity) detection algorithm based on Voronoi…

An open source protein pocket (cavity) detection algorithm based on Voronoi tessellation.

AutoLigand
Desktop

AutoLigand

A method for the prediction of ligand-binding sites in proteins of known…

A method for the prediction of ligand-binding sites in proteins of known structure. AutoLigand makes predictions based strictly on the properties of the receptor, identifying the optimal ligand…

G-LoSA
Desktop

G-LoSA Graph-based Local Structure Alignment

A local structure alignment tool. The known protein-ligand binding-site…

A local structure alignment tool. The known protein-ligand binding-site structure library is searched by G-LoSA to detect binding-site structures with similar geometry and physicochemical properties…

DoGSiteScorer
Web

DoGSiteScorer

An automated pocket detection and analysis tool which can be used for protein…

An automated pocket detection and analysis tool which can be used for protein druggability assessment.

metaPocket
Web

metaPocket

A meta server to identify ligand binding sites on protein surface.

A meta server to identify ligand binding sites on protein surface.

MDpocket
Web

MDpocket

A method providing a fast, free and open-source tool for tracking small…

A method providing a fast, free and open-source tool for tracking small molecule binding sites and gas migration pathways on molecular dynamics (MDs) trajectories or other conformational ensembles.

POCASA
Web

POCASA POcket-CAvity Search Application

An automatic program that implements the algorithm named Roll which can predict…

An automatic program that implements the algorithm named Roll which can predict binding sites by detecting pockets and cavities of proteins of known 3D structure.

KVFinder
Desktop

KVFinder

A highly versatile and easy-to-use tool for cavity prospection and spatial…

A highly versatile and easy-to-use tool for cavity prospection and spatial characterization. KVFinder is a geometrical-based method that has an innovative customization of the search space. It…

PocketFEATURE
Desktop

PocketFEATURE

Focuses on pockets using the FEATURE system for characterizing…

Focuses on pockets using the FEATURE system for characterizing microenvironments. The method is able to recognize several proven distant relationships, and predicts unexpected shared ligand binding.

ConCavity
Desktop
Web

ConCavity

A small molecule binding site prediction algorithm that integrates evolutionary…

A small molecule binding site prediction algorithm that integrates evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities.

pevoSOAR
Dataset

pevoSOAR Pocketbased EVOlutionary Search Of Amino acid Residues

A method based on comparing similarity of protein surfaces. PEVOSOAR predicts…

A method based on comparing similarity of protein surfaces. PEVOSOAR predicts protein functions by solving the problem of uncovering residue substitution pattern due to protein function and…

TRAPP
Web

TRAPP TRAnsient Pockets in Proteins

A tool for tracking, analysis and visualization of protein cavity dynamics…

A tool for tracking, analysis and visualization of protein cavity dynamics using protein motion trajectory or within an ensemble of protein structures. TRAPP is not designed to identify all of a…

PCA
Desktop

PCA PocketAnalyzer

An automated approach to diverse pocket selection. PocketAnalyzer(PCA) combines…

An automated approach to diverse pocket selection. PocketAnalyzer(PCA) combines a geometric algorithm for detecting pockets in proteins with Principal Component Analysis and clustering. This enables…

PocketDepth
Web

PocketDepth

A method for identification of binding sites in proteins. The PocketDepth’s…

A method for identification of binding sites in proteins. The PocketDepth’s method is purely geometry-based and proceeds in two stages, labeling of grid cells with depth factors followed by a depth…

PocketPicker
Desktop

PocketPicker

An automated grid-based technique for the prediction of protein binding pockets…

An automated grid-based technique for the prediction of protein binding pockets that specifies the shape of a potential binding-site with regard to its buriedness. PocketPicker is available as a…

Screen2
Web

Screen2 Surface Cavity REcognition and EvaluatioN

Identifies protein cavities and computing cavity attributes that can be applied…

Identifies protein cavities and computing cavity attributes that can be applied for classification and analysis. Screen2 defines surface cavities geometrically in terms of the empty space between the…

PROPORES
Desktop

PROPORES

A toolkit for identifying pockets, cavities and channels of protein structures.…

A toolkit for identifying pockets, cavities and channels of protein structures. The toolkit was developed in PERL programming language and includes “PoreID” for pore identification,…

ghecom
Web

ghecom grid-based HECOMi finder

A program for finding multi-scale pockets on protein surfaces using…

A program for finding multi-scale pockets on protein surfaces using mathematical morphology.

PLB_SAVE
Web

PLB_SAVE

Predicts protein-ligand binding region by computing features of solid angle,…

Predicts protein-ligand binding region by computing features of solid angle, volume and depth.

Provar
Desktop

Provar Probability of variation

A method for probabalistic scoring of pocket predictions across large sets of…

A method for probabalistic scoring of pocket predictions across large sets of related protein structures. These scores are the overall probabilities of particular atoms or residues being found to be…

LIGSITEcsc
Desktop
Web

LIGSITEcsc

A web server for the automatic identification of pockets on protein surface…

A web server for the automatic identification of pockets on protein surface using the Connolly surface and the degree of conservation. The use of the Connolly surface leads to slight improvements,…

GIRAF
Web

GIRAF Geometric Indexing and Refined Alignment Finder

Achieves search of similar structures of ligand binding sites of proteins by…

Achieves search of similar structures of ligand binding sites of proteins by exploiting database indexing of structural features of local coordinate frames. GIRAF produces refined atom-wise…

SURFNET
Desktop

SURFNET

Generates molecular surfaces and gaps between surfaces from 3D coordinates…

Generates molecular surfaces and gaps between surfaces from 3D coordinates supplied in a PDB-format file. The gap regions can correspond to the voids between two or more molecules, or to the internal…

ODA
Web

ODA Optimal Docking Area

Analyzes a protein surface in search of areas with favorable energy change when…

Analyzes a protein surface in search of areas with favorable energy change when buried upon protein–protein association. ODA identifies continuous surface patches with optimal docking desolvation…

Q-SiteFinder
Web

Q-SiteFinder

A method of ligand binding site prediction. Q-SiteFinder uses the interaction…

A method of ligand binding site prediction. Q-SiteFinder uses the interaction energy between the protein and a simple van der Waals probe to locate energetically favourable binding sites.…

BSR
Web

BSR Binding Site Refinement

Refines ligand-binding regions in protein models using remotely related…

Refines ligand-binding regions in protein models using remotely related templates identified by threading. BSR uses a Support Vector Regression (SVR) model that selects correct binding site…

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