Protein-ligand docking is a key computational method in the design of starting points for the drug discovery process.

MOLS
Desktop

MOLS Mutually Orthogonal Latin Squares

Performs an efficient and exhaustive conformational search of the…

Performs an efficient and exhaustive conformational search of the multi-dimensional potential energy hypersurface of an oligopeptide, and locates all its low energy conformations. MOLS is a peptide…

BINANA
Desktop

BINANA BINing ANAlyzer

A Python package for analyzing ligand binding. BINANA automates the potentially…

A Python package for analyzing ligand binding. BINANA automates the potentially tedious task of characterizing ligand-receptor complexes for binding characteristics like hydrogen-bond, hydrophobic,…

CLC Drug…
Desktop

CLC Drug Discovery

A virtual lab bench developed specifically for bench chemists and biochemists,…

A virtual lab bench developed specifically for bench chemists and biochemists, to inspire and facilitate drug design improvements. CLC Drug Discovery gives access to atomic level insights in…

DOCK
Desktop

DOCK

A package to recreate experimentally determined binding poses. DOCK is a…

A package to recreate experimentally determined binding poses. DOCK is a dynamic tool for a wide variety of structure-based drug design projects both because of the range of currently available…

JADOPPT
Desktop

JADOPPT Java based AutoDock Preparing and Processing Tool

A visual tool for analyzing and comparing multiple docking results. JADOPPT…

A visual tool for analyzing and comparing multiple docking results. JADOPPT focuses on reducing the dimensionality problem by hierarchically selecting representative poses for each docked molecule.…

PyDPI
Desktop

PyDPI Drug-Protein Interaction with Python

A comprehensive python package to emphasize the integration of chemoinformatics…

A comprehensive python package to emphasize the integration of chemoinformatics and bioinformatics into a molecular informatics platform for drug discovery. PyDPI is a powerful toolkit for computing…

LigSearch
Web

LigSearch

A web server aimed at predicting ligands that might bind to and stabilize a…

A web server aimed at predicting ligands that might bind to and stabilize a given protein. LigSearch utilizes resources such as ChEMBL, ChEBI, KEGG and various other servers to find potential…

DrugMiner
Data

DrugMiner

Identifies whether one protein is druggable or not. DrugMiner has provided an…

Identifies whether one protein is druggable or not. DrugMiner has provided an opportunity for researchers to check if their own-synthesized proteins are druggable. It was developed by analyzing…

SiteComp
Web

SiteComp

A server for ligand binding site analysis in protein structures. SiteComp uses…

A server for ligand binding site analysis in protein structures. SiteComp uses molecular interaction fields (MIFs) as descriptors of small molecule ligand binding sites. MIFs describe the spatial…

DockThor
Web

DockThor

Facilitates and enables the use of the docking methodology by the academic…

Facilitates and enables the use of the docking methodology by the academic community. DockThor program is a flexible-ligand and rigid-receptor grid based method that employs a multiple solution…

Dockovalent
Web

Dockovalent

Studies large virtual libraries of electrophilic small molecules. DOCKovalent…

Studies large virtual libraries of electrophilic small molecules. DOCKovalent exhaustively samples all poses and ligand conformations with respect to the covalent bond to the target nucleophile,…

LeView
Desktop

LeView Ligand Environment Viewer

Generates 2D diagrams of biomacromolecule/ligand interactions. LeView produces…

Generates 2D diagrams of biomacromolecule/ligand interactions. LeView produces customised and high-quality figures, with a good compromise between a faithful representation of the 3D data (structures…

Twilight
Desktop

Twilight

Aims to simplify electron-density-map-based visualization, analysis,…

Aims to simplify electron-density-map-based visualization, analysis, validation, annotation and correction of ligand molecules found in protein structures determined by X-ray crystallography.…

Ligalign
Desktop

Ligalign Automated Ligand-Based Active Site Alignment

An automated system for flexible ligand alignment and analysis. The LigAlign…

An automated system for flexible ligand alignment and analysis. The LigAlign system extracts the set of ligands that is most self- consistent across the submitted structures. LigAlign automatically…

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…

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…

MANORAA
Web

MANORAA Mapping Analogous Nuclei Onto Residue And Affinity

A web service for identification of ligand & residue interactions, SNP and…

A web service for identification of ligand & residue interactions, SNP and pathway analysis. Manoraa allows the users to input the chemical fragments and present all the unique molecular…

MIEC-SVM
Desktop

MIEC-SVM Molecular Interaction Energy Component & Support Vector Machine

A structure-based method for predicting protein recognition specificity. To…

A structure-based method for predicting protein recognition specificity. To make the method more accessible to the scientific community, we construct a pipeline to facilitate the use of existing…

Alloscore
Web

Alloscore

Provides a user-friendly interface to predict the binding affinities of…

Provides a user-friendly interface to predict the binding affinities of allosteric ligand-protein interactions. Furthermore, critical energy contributions that contribute to allosteric binding are…

ProBiS-ligands
Web

ProBiS-ligands

A web server for prediction of ligands based on detected local structural…

A web server for prediction of ligands based on detected local structural similarities in proteins. ProBiS-ligands requires a query protein structure or a query binding site, and this is first…

Glide
Desktop

Glide

A package which approximates a complete search of the conformational,…

A package which approximates a complete search of the conformational, orientational, and positional space of the ligand in a given receptor. Glide offers the full range of quick and accurate options,…

AutoDock Vina
Desktop

AutoDock Vina

An open-sourcepackage for molecular docking and virtual screening. It achieves…

An open-sourcepackage for molecular docking and virtual screening. It achieves an approximately two orders of magnitude speed-up compared to the molecular docking software previously developed in…

ChemProt
Data

ChemProt

A publicly available compilation of chemical-protein-disease annotation…

A publicly available compilation of chemical-protein-disease annotation resources that enables the study of systems pharmacology for a small molecule across multiple layers of complexity from…

PLIff
Desktop

PLIff Protein-Ligand Informatics force field

Captures a wide range of interaction types, including special interactions that…

Captures a wide range of interaction types, including special interactions that are often poorly described by standard force fields. PLiff performs at least as well as state-of-the art scoring…

PocketOptimizer
Desktop

PocketOptimizer

Predicts mutations in the binding pocket of proteins, which increase the…

Predicts mutations in the binding pocket of proteins, which increase the affinity of the protein to a given small molecule ligand. PocketOptimizer is a method for the computational design of…

DUck
Desktop

DUck Dynamic Undocking

A method to calculate the work necessary to reach a quasi-bound state at which…

A method to calculate the work necessary to reach a quasi-bound state at which the ligand has just broken the most important native contact with the receptor. DUck includes only the minimal subset of…

Patch-Surfer
Web

Patch-Surfer

Compares a query pocket to known ligand binding pockets and predicts binding…

Compares a query pocket to known ligand binding pockets and predicts binding ligand molecules for the query. PatchSurfer2.0 recognizes pockets for the same ligand by identifying common local regions…

SPOT-Ligand
Web

SPOT-Ligand

Integrates ligand similarity by Tanimoto coefficient and receptor similarity by…

Integrates ligand similarity by Tanimoto coefficient and receptor similarity by protein structure alignment program SPalign. SPOT-Ligand was found to yield a consistent performance in DUD and DUD-E…

Vinardo
Desktop

Vinardo Vina RaDii Optimized

A scoring function which shares component terms with the Vina scoring function:…

A scoring function which shares component terms with the Vina scoring function: steric interactions, hydrophobic interactions, and non-directional H-bonds. Despite sharing component terms, Vinardo…

systemsDock
Web

systemsDock

A web service enabling drug developers to carry out network pharmacology-based…

A web service enabling drug developers to carry out network pharmacology-based prediction and analysis by integrating results from structural biology with systems biology. Its user-friendly GUI…

BSP-SLIM
Web

BSP-SLIM

A blind molecular docking method on low-resolution protein structures. BSP-SLIM…

A blind molecular docking method on low-resolution protein structures. BSP-SLIM first identifies putative ligand binding sites by structurally matching the target to the template holo-structures. The…

PSOVina
Desktop

PSOVina

A fast docking tool based on the efficient optimization algorithm of particle…

A fast docking tool based on the efficient optimization algorithm of particle swarm intelligence and the framework of AutoDock Vina. In our rigorous docking tests using the PDBBind data set and the…

NBDB
Data

NBDB Nucleotide Binding Data Base

Provides profiles of elementary functional loops (EFLs) involved in binding of…

Provides profiles of elementary functional loops (EFLs) involved in binding of nucleotide-containing ligands. Each EFL in form of a PSSM (position-specific scoring matrix) profile is complemented…

KLIFS
Data

KLIFS Kinase-Ligand Interaction Fingerprints and Structures database

Revolves around the protein structure of catalytic kinase domains and the way…

Revolves around the protein structure of catalytic kinase domains and the way kinase inhibitors can interact with them. Based on the underlying systematic and consistent protocol all (currently human…

Panther
Desktop

Panther

An ultrafast multipurpose docking tool. In Panther, a simple…

An ultrafast multipurpose docking tool. In Panther, a simple shape-electrostatic model of the ligand-binding area of the protein is created by utilizing the protein crystal structure. The features of…

FlexAID
Desktop

FlexAID

A small-molecule docking algorithm that accounts for target side-chain…

A small-molecule docking algorithm that accounts for target side-chain flexibility and utilizes a soft scoring function, i.e. one that is not highly dependent on specific geometric criteria, based on…

NRGsuite
Desktop

NRGsuite

A PyMOL plugin that permits the detection of surface cavities in proteins,…

A PyMOL plugin that permits the detection of surface cavities in proteins, their refinements, calculation of volume and use, individually or jointly, as target binding-sites for docking simulations…

SInCRe
Data

SInCRe Structural Interactome Computational Resource

An integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates…

An integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates information on protein sequences, domain assignments, functional annotation and 3D structural information along with…

SimiCon
Web

SimiCon

A web server designed for an automated identification of equivalent…

A web server designed for an automated identification of equivalent protein-ligand atomic contacts in different conformational models of a complex. The contacts are computed with internal coordinate…

PLATINUM
Web

PLATINUM Protein–Ligand ATtractions Investigation NUMerically

A web app designed for analysis and visualization of hydrophobic/hydrophilic…

A web app designed for analysis and visualization of hydrophobic/hydrophilic properties of biomolecules supplied as 3D-structures. Furthermore, PLATINUM provides a number of tools for quantitative…

CRDOCK
Desktop

CRDOCK

An ultrafast docking and virtual screening program that contains (1) a search…

An ultrafast docking and virtual screening program that contains (1) a search engine that can use a variety of sampling methods and an initial energy evaluation function, (2) several energy…

SODOCK
Desktop

SODOCK

An optimization algorithm based on particle swarm optimization (PSO) for…

An optimization algorithm based on particle swarm optimization (PSO) for solving flexible protein-ligand docking problems. PSO is a population-based search algorithm. It is very simple and efficient.…

eSimDock
Web

eSimDock

A similarity-based approach to ligand docking and binding affinity prediction.…

A similarity-based approach to ligand docking and binding affinity prediction. Given the receptor structure, anchor ligand and a query compound, eSimDock employs machine learning and a set of…

eFindSite
Desktop
Web

eFindSite

A ligand binding site prediction and virtual screening algorithm that detects…

A ligand binding site prediction and virtual screening algorithm that detects common ligand binding sites in a set of evolutionarily related proteins identified by 10 threading/fold recognition…

CovalentDock
Desktop
Web

CovalentDock

Allows the researchers and scientists to perform protein-ligand covalent…

Allows the researchers and scientists to perform protein-ligand covalent docking. In contrast to conventional molecular docking protocols, covalent docking will allow the formation of covalent…

PLIP
Desktop
Web

PLIP Protein-Ligand Interaction Profiler

A web service for fully automated detection and visualization of relevant…

A web service for fully automated detection and visualization of relevant non-covalent protein-ligand contacts in 3D structures. PLIP stands out by offering publication-ready images, PyMOL session…

QuickVina
Desktop

QuickVina

Inherits both the speed of QVina 1 and the reliability of the original Vina.…

Inherits both the speed of QVina 1 and the reliability of the original Vina. The efficacy of QVina 2 on the core set of PDBbind 2014 was tested. With the default exhaustiveness level of Vina (i.e.…

aCSM
Desktop

aCSM atomic Cutoff Scanning Matrix

Receptor-ligand interactions are a central phenomenon in most biological…

Receptor-ligand interactions are a central phenomenon in most biological systems. aCSM is a graph-based-binding pocket signature that proved to be efficient and effective in handling large-scale…

Platinum
Data

Platinum

Studies the impacts of missense mutations on the interaction of ligands with…

Studies the impacts of missense mutations on the interaction of ligands with the proteome. This manually curated, literature-derived database, comprising over 1000 mutations, associates for the first…

Rcpi
Desktop

Rcpi Compound-Protein Interaction with R

A freely available R/Bioconductor package for complex molecular representation…

A freely available R/Bioconductor package for complex molecular representation from drugs, proteins and more complex interactions, including protein-protein and compound-protein interactions. Rcpi…

PiPreD
Desktop

PiPreD

A computational, structure and knowledge-based, approach to model orthosteric…

A computational, structure and knowledge-based, approach to model orthosteric peptides to target protein-protein interactions (PPIs). PiPreD relies on a precompiled and bespoken library of structural…

SEABED
Cloud

SEABED

Integrates a variety of docking and QSAR techniques in a user-friendly…

Integrates a variety of docking and QSAR techniques in a user-friendly environment. SEABED goes beyond the basic docking and QSAR web tools and implements extended functionalities like receptor…

LIGSIFT
Desktop

LIGSIFT

An open-source ligand structure alignment and virtual screening algorithm that…

An open-source ligand structure alignment and virtual screening algorithm that uses Gaussian molecular shape overlay for fast small molecule alignment and a size-independent scoring function for…

CSAR
Data

CSAR Community Structure-Activity Resource

Provides experimental datasets of crystal structures and binding affinities for…

Provides experimental datasets of crystal structures and binding affinities for diverse protein-ligand complexes. Some datasets will be generated in house at Michigan while others will be collected…

LigBase
Data

LigBase

This is a database of ligand binding proteins aligned to structural templates.

This is a database of ligand binding proteins aligned to structural templates.

SwissDock
Web
Desktop

SwissDock

A web server dedicated to the docking of small molecules on target proteins.…

A web server dedicated to the docking of small molecules on target proteins. SwissDock aims at extending the use of protein-small molecule docking software far beyond experts in the field by…

TargetS
Web

TargetS

A ligand-specific template-free predictor for targeting protein-ligand binding…

A ligand-specific template-free predictor for targeting protein-ligand binding sites from primary sequences.

BINDSURF
Desktop

BINDSURF

A fast blind methodology for the determination of protein binding sites…

A fast blind methodology for the determination of protein binding sites depending on the ligand, that uses the massively parallel architecture of GPUs for fast pre-screening of large ligand databases.

rDock
Desktop

rDock

A fast and versatile Open Source docking program that can be used to dock small…

A fast and versatile Open Source docking program that can be used to dock small molecules against proteins and nucleic acids.

PLIC
Data

PLIC

Clusters of similar binding sites in the PDB and analysis of various type of…

Clusters of similar binding sites in the PDB and analysis of various type of interactions within the clusters.

PoSSuM
Web

PoSSuM Pocket Similarity Search using Multiple-Sketches

A database for detecting similar small-molecule binding sites on proteins.…

A database for detecting similar small-molecule binding sites on proteins. Since its initial release in 2011, PoSSuM has grown to provide information related to 49 million pairs of similar binding…

Pocketome
Data

Pocketome

Allows searching for the sites of interest, analysis of conformational…

Allows searching for the sites of interest, analysis of conformational clusters, important residues, binding compatibility matrices and interactive visualization of the ensembles using the ActiveICM…

sc-PDB
Data

sc-PDB

A comprehensive and up-to-date selection of ligandable binding sites of the…

A comprehensive and up-to-date selection of ligandable binding sites of the Protein Data Bank. Sites are defined from complexes between a protein and a pharmacological ligand. The database provides…

FlexX
Desktop

FlexX

Predicts the geometry of the protein-ligand complex within a few seconds.

Predicts the geometry of the protein-ligand complex within a few seconds.

FRED
Desktop

FRED

Performs a systematic, exhaustive, nonstochastic examination of all possible…

Performs a systematic, exhaustive, nonstochastic examination of all possible poses within the protein active site, filters for shape complementarity and pharmacophoric features.

GOLD
Desktop

GOLD

Enables you to make confident binding mode predictions, and achieve high…

Enables you to make confident binding mode predictions, and achieve high database enrichments.

MADAMM
Desktop

MADAMM

Allows flexibilization of both the receptor and the ligand during a multistaged…

Allows flexibilization of both the receptor and the ligand during a multistaged docking with an automated molecular modeling protocol.

Surflex-Dock
Desktop

Surflex-Dock

A fully automatic flexible molecular docking algorithm.

A fully automatic flexible molecular docking algorithm.

UCSF Chimera
Desktop

UCSF Chimera

A highly extensible program for interactive visualization and analysis of…

A highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking…

DINC
Web

DINC

Uses an AutoDock-based incremental docking protocol to dock large ligands.

Uses an AutoDock-based incremental docking protocol to dock large ligands.

GIANT
Web

GIANT

Users can interactively analyze protein-small ligand binding modes with…

Users can interactively analyze protein-small ligand binding modes with statistically determined interaction patterns rather than relying on a priori knowledge of the users.

idock
Web

idock

A multithreaded virtual screening tool for flexible ligand docking.

A multithreaded virtual screening tool for flexible ligand docking.

iview
Web

iview

An easy-to-use interactive WebGL visualizer of protein-ligand complex.

An easy-to-use interactive WebGL visualizer of protein-ligand complex.

LigPlot+
Desktop

LigPlot+

Multiple ligand-protein interaction diagrams for drug discovery.

Multiple ligand-protein interaction diagrams for drug discovery.

PoseView
Web

PoseView

Automatically creates two-dimensional diagrams of complexes with known 3D…

Automatically creates two-dimensional diagrams of complexes with known 3D structure according to chemical drawing conventions.

3DLigandSite
Web

3DLigandSite

An automated method for the prediction of ligand binding sites.

An automated method for the prediction of ligand binding sites.

COACH
Web

COACH

A meta-server approach to protein-ligand binding site prediction.

A meta-server approach to protein-ligand binding site prediction.

FunFOLD
Web

FunFOLD

An improved automated method for the prediction of ligand binding residues…

An improved automated method for the prediction of ligand binding residues using 3D models of proteins.

GalaxySite
Web

GalaxySite

Prediction of ligand binding site of a query protein is performed.

Prediction of ligand binding site of a query protein is performed.

Multiconf-DOCK
Desktop

Multiconf-DOCK

Generates multiple conformers for small organic molecules using DOCK5.

Generates multiple conformers for small organic molecules using DOCK5.

Cyscore
Desktop

Cyscore

An empirical scoring function for accurate protein-ligand binding affinty…

An empirical scoring function for accurate protein-ligand binding affinty prediction.

CREDO
Data

CREDO

A publicly available database of protein-ligand interactions, which represents…

A publicly available database of protein-ligand interactions, which represents contacts as structural interaction fingerprints, implements novel features and is completely scriptable through its…

HIC-Up
Data

HIC-Up

Contains information about hetero-compounds encountered in files from the…

Contains information about hetero-compounds encountered in files from the Protein Data Bank (PDB).

KEGG LIGAND
Data

KEGG LIGAND

Contains our knowledge on the universe of chemical substances and reactions…

Contains our knowledge on the universe of chemical substances and reactions that are relevant to life.

MATADOR
Data

MATADOR

A resource for protein-chemical interactions. MATADOR differs from other…

A resource for protein-chemical interactions. MATADOR differs from other resources such as DrugBank in its inclusion of as many direct and indirect interactions as we could find. In contrast,…

The PDBbind…
Data

The PDBbind database

The PDBbind database is designed to provide a collection of experimentally…

The PDBbind database is designed to provide a collection of experimentally measured binding affinity data (Kd, Ki, and IC50) exclusively for the protein-ligand complexes available in the Protein Data…

BindingDB
Data

BindingDB

A publicly accessible database of experimental protein-small molecule…

A publicly accessible database of experimental protein-small molecule interaction data. Its collection of over a million data entries derives primarily from scientific articles and, increasingly, US…

BioLiP
Data

BioLiP

A semi-manually curated database for high-quality, biologically relevant…

A semi-manually curated database for high-quality, biologically relevant ligand-protein binding interactions.

FireDB
Data

FireDB

A curated inventory of catalytic and biologically relevant small ligand-binding…

A curated inventory of catalytic and biologically relevant small ligand-binding residues culled from the protein structures in the Protein Data Bank.

AffinDB
Data

AffinDB

Its purpose is to provide direct and free access to the experimental affinity…

Its purpose is to provide direct and free access to the experimental affinity of a given complex structure.

Binding MOAD
Data

Binding MOAD Binding Mother of All Databases

A subset of the Protein Data Bank (PDB), containing every high-quality example…

A subset of the Protein Data Bank (PDB), containing every high-quality example of ligand-protein binding. Binding MOAD's goal is to be the largest collection of well resolved protein crystal…

LigDig
Web

LigDig

A webserver designed to answer questions that previously required several…

A webserver designed to answer questions that previously required several independent queries to diverse data-sources. It also performs basic manipulations and analyses of the structures of…

webPDBinder
Web

webPDBinder

A web server for the identification of small ligand-binding sites in a protein…

A web server for the identification of small ligand-binding sites in a protein structure. webPDBinder searches a protein structure against a library of known binding sites and a collection of control…

LigASite
Data

LigASite LIGand Attachment SITE

A gold-standard dataset of binding sites in 550 proteins of known structures.…

A gold-standard dataset of binding sites in 550 proteins of known structures. LigASite consists exclusively of biologically relevant binding sites in proteins for which at least one apo- and one…

PLD
Data

PLD Protein Ligand Database

A publicly available web-based database that aims to provide further…

A publicly available web-based database that aims to provide further understanding of protein-ligand interactions. The PLD contains biomolecular data including calculated binding energies, Tanimoto…

VMD
Desktop

VMD

A molecular visualization program for displaying, animating, and analyzing…

A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

PLID
Data

PLID Protein Ligand Interaction Database

A comprehensive database of physico-chemical properties, quantum mechanical…

A comprehensive database of physico-chemical properties, quantum mechanical descriptors and the residues present in the active site of proteins.

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