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Protein-ligand docking tools

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

BindingDB
Dataset

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…

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,…

ChemProt
Dataset

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…

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…

sc-PDB
Dataset

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…

RF-Score
Desktop

RF-Score

Introduces a substantial improvement over classical scoring functions. RF-Score…

Introduces a substantial improvement over classical scoring functions. RF-Score is a machine-learning scoring function that was constructed in an entirely data-driven manner by circumventing the need…

VMD
Desktop

VMD

Displays molecules containing any number of atoms and is similar to other…

Displays molecules containing any number of atoms and is similar to other molecular visualization programs in its basic capabilities. VMD has been developed for interactive graphical display of…

AutoDock
Desktop

AutoDock

Provides automated docking tools. AutoDock uses a grid-based method to allow a…

Provides automated docking tools. AutoDock uses a grid-based method to allow a rapid evaluation of the binding energy of trial conformations. The software can predict bound conformations and binding…

UCSF Chimera
Desktop

UCSF Chimera

Permits to interactively visualize and analyse molecular structures and related…

Permits to interactively visualize and analyse molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and…

OOMMPPAA
Web
Desktop

OOMMPPAA

Allows easy analysis and interpretation of protein–ligand interaction data.…

Allows easy analysis and interpretation of protein–ligand interaction data. OOMMPPAA includes protein–ligand activity data with protein–ligand structural data utilizing 3D matched molecular…

AutoDock Vina
Desktop

AutoDock Vina

Allows molecular docking and virtual screening. AutoDock Vina is one of the two…

Allows molecular docking and virtual screening. AutoDock Vina is one of the two generations of distributions of AutoDock. This software uses a sophisticated gradient optimization method in its local…

3DLigandSite
Web

3DLigandSite

Predicts ligand-binding sites. 3DLigandSite is a web server that uses ligands…

Predicts ligand-binding sites. 3DLigandSite is a web server that uses ligands from similar structures to make predictions. Options are available to modify the display of the whole protein, predicted…

MATADOR
Dataset

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,…

WONKA
Web
Desktop

WONKA

Facilitates the analysis and interpretation of protein–ligand interaction…

Facilitates the analysis and interpretation of protein–ligand interaction data. WONKA is able to analyse ensembles of protein–ligand structures and to find trends within a set of structures of…

PHASE
Desktop

PHASE

Offers solution for pharmacophore perception, quantitative structure-activity…

Offers solution for pharmacophore perception, quantitative structure-activity relationship (QSAR) model development, and 3D database screening. PHASE aims to suggest a set of plausible models that…

Ligandbook
Dataset

Ligandbook

Provides force-field parameters of small and drug-like molecules for all major…

Provides force-field parameters of small and drug-like molecules for all major all-atom force fields. Ligandbook aims to enable parameter re-use and simulation reproducibility by (1) facilitating the…

BioLiP
Dataset

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.

idock
Web
Desktop

idock

Allows flexible ligand docking. Idock is a virtual screening tool that consists…

Allows flexible ligand docking. Idock is a virtual screening tool that consists of two basic components: a scoring function to predict the binding affinity, and an optimization algorithm to explore…

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…

Binding MOAD
Dataset

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…

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,…

LigPlot+
Desktop

LigPlot+

Automatically generates 2D ligand-protein interaction diagrams. LigPlot+ is a…

Automatically generates 2D ligand-protein interaction diagrams. LigPlot+ is a graphical front-end to the LIGPLOT and DIMPLOT programs. The software allows the 2D representation of multiple ligand…

SiteMap
Desktop

SiteMap

Analyzes and identifies binding sites, and predicts target druggability.…

Analyzes and identifies binding sites, and predicts target druggability. SiteMap studies the druggability of proteins as measured by their ability to bind passively absorbed small molecules tightly.…

SA-conf
Desktop

SA-conf

Allows analysis of the structural variability landscape for a given protein.…

Allows analysis of the structural variability landscape for a given protein. SA-conf is a structural alphabet (SA)-based tool that facilitates the analysis and comparison of large and diverse…

Pocketome
Dataset

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…

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.…

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…

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…

DrugMiner
Dataset

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…

GalaxySite
Web

GalaxySite

Predicts binding sites of non-metal ligands. GalaxySite is a web server that…

Predicts binding sites of non-metal ligands. GalaxySite is a web server that employs molecular docking. Binding ligand is predicted using a similarity-based method, and the protein structure is…

e-pharmacophore…
Desktop

e-pharmacophores

Generates energy-optimized pharmacophores. e-pharmacophores is based on mapping…

Generates energy-optimized pharmacophores. e-pharmacophores is based on mapping of the energetic terms from the Glide XP scoring function onto atom centers. It was tested by screening a set of 30…

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.

The PDBbind…
Dataset

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…

FEP+
Desktop

FEP+ Free Energy Perturbation

Allows to set up the desired perturbations without requiring expert knowledge…

Allows to set up the desired perturbations without requiring expert knowledge of the complex calculations that are automated behind the scenes. FEP+ enables 2 to 4 ligands to be scored per day on a…

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…

KLIFS
Dataset

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…

FireDB
Dataset

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
Dataset

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.

COACH
Web

COACH COnsensus ApproaCH

Allows protein-ligand binding site (LBS) prediction. COACH is a consensus…

Allows protein-ligand binding site (LBS) prediction. COACH is a consensus approach that combines the multiple prediction results of algorithms from TM-SITE, S-SITE, COFACTOR, FINDSITE and ConCavity.…

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…

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…

NBDB
Dataset

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…

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…

NLDB
Dataset

NLDB Natural Ligand DataBase

Offers collected and predicted 3D protein–ligand interactions for the…

Offers collected and predicted 3D protein–ligand interactions for the enzymatic reactions of metabolic pathways registered in KEGG. NLDB contains 68,551 natural, 28,441 analog and 64,204 ab initio…

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…

Cyscore
Desktop

Cyscore

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

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

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.

Phosfinder
Web

Phosfinder

Provides a web server for the prediction of phosphate binding sites in protein…

Provides a web server for the prediction of phosphate binding sites in protein structures. The Phosfinder server offers a user-friendly version of the Pfinder method, enriched with the possibility to…

DOCKTITE
Desktop

DOCKTITE

Allows covalent docking and virtual screening in molecular operating…

Allows covalent docking and virtual screening in molecular operating environment (MOE). DOCKTITE combines the knowledge-based scoring function drug score extended (DSX) and the empirical scoring…

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.

SCORPIO
Dataset

SCORPIO Structure-Calorimetry of Reported Protein Interactions Online

Provides access to complete sets of thermodynamic data for protein-ligand…

Provides access to complete sets of thermodynamic data for protein-ligand complexes that have had their structures resolved. SCORPIO contains a wide variety of ligands ranging from natural…

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…

TopologyNet
Web

TopologyNet

Allows to predict binding affinity and protein stability change upon mutation.…

Allows to predict binding affinity and protein stability change upon mutation. TopologyNet is a multi-task multichannel topological convolutional neural network (MM-TCNN) framework. The software…

AutoShim
Desktop

AutoShim

Creates a target-specific scoring functions to address the limited affinity…

Creates a target-specific scoring functions to address the limited affinity prediction of general-purpose scoring functions. AutoShim defines and evaluates specific interactions between a bound…

MedusaScore
Algorithm

MedusaScore

Allows to evaluate protein-ligand binding. MedusaScore is a scoring function…

Allows to evaluate protein-ligand binding. MedusaScore is a scoring function that describes the protein-ligand binding using physical interaction model. The function includes an explicit…

Induced Fit
Desktop

Induced Fit

Accounts for receptor flexibility in ligand-receptor docking by iteratively…

Accounts for receptor flexibility in ligand-receptor docking by iteratively combining rigid receptor docking with protein structure prediction and refinement. Induced Fit generates viable receptor…

Endocrine…
Web

Endocrine Disruptome

Detects endocrine disruption potential of compounds. Endocrine Disruptome is an…

Detects endocrine disruption potential of compounds. Endocrine Disruptome is an open source prediction tool which allows users to practice docking experiments using 12 different human nuclear…

PLEIC-SVM
Algorithm

PLEIC-SVM Protein-Ligand Empirical Interaction Components Support Vector Machine

Maps protein-ligand binding interactions on protein pocket residues. PLEIC-SVM…

Maps protein-ligand binding interactions on protein pocket residues. PLEIC-SVM is a classification model built as a post-docking process for virtual screening that uses active and inactive…

CovDock
Desktop

CovDock

Allows prediction and scoring of covalently bound ligands. CovDock is a…

Allows prediction and scoring of covalently bound ligands. CovDock is a covalent docking protocol built upon a foundation of the Glide docking algorithm and Prime structure refinement methodology for…

VinaMPI
Desktop

VinaMPI Vina Message Passing Interface

Facilitates multiple receptor screens with a large number of compounds…

Facilitates multiple receptor screens with a large number of compounds utilizing the largest number of processors in order to reduce the time-to-completion. VinaMPI is a massively parallel Message…

TargetATPsite
Web

TargetATPsite

Predicts protein- Adenosine-5’ -triphosphate (ATP) binding site.…

Predicts protein- Adenosine-5’ -triphosphate (ATP) binding site. TargetATPsite can report binding pockets from the predicted binding residues with a spatial clustering process. It uses an image…

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…

Platinum
Dataset

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…

Surflex-Dock
Desktop

Surflex-Dock

Uses procedures for pre-docking minimization and post-docking all-atom…

Uses procedures for pre-docking minimization and post-docking all-atom in-pocket optimization. Surflex employs an active site ligand as a target to generate putative poses of molecules or molecular…

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.…

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…

iview
Web

iview

Allows visualization of protein-ligand complex. iview is an interactive WebGL…

Allows visualization of protein-ligand complex. iview is an interactive WebGL visualizer of protein-ligand complex, featuring three special effects in virtual reality settings and four surface…

CREDO
Dataset

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
Dataset

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).

PostDOCK
Algorithm

PostDOCK

Allows to evaluate and rank ligand-receptor complexes. PostDOCK is a…

Allows to evaluate and rank ligand-receptor complexes. PostDOCK is a post-processing filter aiming to improve the results obtained by the scoring methods in docking by adding a post-processing filter…

ContPro
Web

ContPro

Calculates amino acid contact distances in proteins at different distance…

Calculates amino acid contact distances in proteins at different distance threshold from the 3 Dimensional (3D)-structure of the protein. ContPro calculates the distance between selected protein…

MORDOR
Desktop

MORDOR MOlecular Recognition with a Driven dynamics OptimizeR

Allows creation of binding site and docking. MORDOR is a software which…

Allows creation of binding site and docking. MORDOR is a software which contains all of the tools for virtual screening. The software can perform the main docking using its own energetic and…

ID-Score
Algorithm

ID-Score

Exhibits better ability in discriminating analogues than other selective seven…

Exhibits better ability in discriminating analogues than other selective seven scoring functions in a sensitive test. ID-Score is an empirical scoring function derived based on a comprehensive set of…

SCAR
Desktop

SCAR Steric-Clashes Alleviating Receptor

Allows covalent docking. SCAR eliminates steric clashes between covalently…

Allows covalent docking. SCAR eliminates steric clashes between covalently bonding atoms thank to silico protein mutagenesis. It takes advantage of the already well-developed non-covalent docking…

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.

Multiconf-DOCK
Desktop

Multiconf-DOCK

Generates several conformers for small organic molecules. Multiconf-DOCK was…

Generates several conformers for small organic molecules. Multiconf-DOCK was developed for small molecule multi-conformer generation that requires as starting point the 3D structure of each input…

CHARMMing
Web

CHARMMing CHARMM INterface and Graphics

Provides a user-friendly interface for the preparation, submission, monitoring,…

Provides a user-friendly interface for the preparation, submission, monitoring, and visualization of molecular simulations. CHARMMing is a web portal for the CHARMM macromolecular modeling package.…

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…

LPIcom
Web

LPIcom

Permits analysis and prediction of interacting amino acids for various ligands.…

Permits analysis and prediction of interacting amino acids for various ligands. LPIcom provides different modules identified as ‘analysis of binding sites’, ‘comparison of multiple binding…

Haptimol_RD
Desktop

Haptimol_RD

Enables the study of large systems such as when two proteins interact.…

Enables the study of large systems such as when two proteins interact. Haptimol_RD is an interactive haptics-assisted docking application that can facilitate, at haptic refresh rates, the study of…

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…

AMMOS
Web

AMMOS Automatic Molecular Mechanics Optimization for in silico Screening

Treats of efficient computational refinement of protein-small organic molecule…

Treats of efficient computational refinement of protein-small organic molecule complexes. The AMMOS2 web server aims to providing at the scientific community a free and user-friendly…

GenProBiS
Web

GenProBiS

Maps sequence variants to protein structures from the Protein Data Bank (PDB),…

Maps sequence variants to protein structures from the Protein Data Bank (PDB), and further to protein–protein, protein–nucleic acid, protein–compound, and protein–metal ion binding sites.…

LigParGen
Web

LigParGen

Provides an intuitive interface for generating OPLS-AA/1.14*CM1A(-LBCC) force…

Provides an intuitive interface for generating OPLS-AA/1.14*CM1A(-LBCC) force field (FF) parameters for organic ligands. LigParGen is a web server which generates ligand parameters for common…

Spresso
Desktop

Spresso

Utilizes the concept of compound decomposition from a previous docking program…

Utilizes the concept of compound decomposition from a previous docking program and expands the concept by allowing re-use of fragment-docking results for analysis of different target compounds…

BAPPL
Web

BAPPL Binding Affinity Prediction of Protein-Ligand

Ensures transferability across diverse systems and has been validated on a…

Ensures transferability across diverse systems and has been validated on a heterogenous dataset of 161 complexes consisting of 55 unique protein targets. BAPPL computes the binding free energy of a…

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…

@TOME-2
Web

@TOME-2

Allows fold recognition, template selection, structural alignment editing,…

Allows fold recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation. @TOME-2 is dedicated to protein structure modeling and small ligand…

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…

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…

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
Desktop

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…

QPLD
Desktop

QPLD QM-Polarized Ligand Docking

Combines the accuracy of QSite and the docking power of Glide. The QPLD…

Combines the accuracy of QSite and the docking power of Glide. The QPLD algorithm starts with a Glide docking job which creates different geometrically unique protein-ligand complexes. Then, QSite…

FINDSITE(comb)
Web

FINDSITE(comb)

Makes the screening of millions of compounds across entire proteomes feasible.…

Makes the screening of millions of compounds across entire proteomes feasible. FINDSITE(comb) is an online service. It has virtual screening accuracy better than the best docking method under the…

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…

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…

LISA
Algorithm

LISA Ligand Identification Scoring Algorithm

Evaluates binding affinity between different protein and ligand pairs. LISA is…

Evaluates binding affinity between different protein and ligand pairs. LISA is an empirical scoring function that is readily applicable to de novo drug design. The algorithm uses different models to…

Pose & Rank
Web

Pose & Rank

Scores protein-ligand complexes. Pose & Rank is a free service using two…

Scores protein-ligand complexes. Pose & Rank is a free service using two atomic distance-dependent statistical scoring functions: PoseScore and RankScore. PoseScore was optimized for recognizing…

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…

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…

OSML
Web

OSML On-Site Model for Ligand binding sites prediction

Predicts protein-ligand binding sites. OSML constructs query-driven prediction…

Predicts protein-ligand binding sites. OSML constructs query-driven prediction model and optimizes it before the prediction task. It is able to perform protein-ligand binding sites prediction for ten…

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…

PoseView
Web
Desktop

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.

PLIC
Dataset

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.

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…

PharmBench
Dataset

PharmBench

Contains 81 targets, 960 ligands aligned using their co-crystallized protein…

Contains 81 targets, 960 ligands aligned using their co-crystallized protein targets. PharmBench is based on known pharmaceutically relevant co-crystallized protein ligand complexes, which were…

TargetVita
Web

TargetVita

Predicts protein-vitamin binding residues using protein sequences. TargetVita…

Predicts protein-vitamin binding residues using protein sequences. TargetVita uses multiple features derived from protein sequences and effectively ensembling heterogeneous support vector machine…

Sanjeevini
Web

Sanjeevini

Provides a freely accessible state of the art software suite for protein and…

Provides a freely accessible state of the art software suite for protein and DNA targeted lead molecule discovery. Sanjeevini builds in several features, including automated detection of active…

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…

CPASS
Desktop

CPASS Comparison of Protein Active Site Structures

Identifies similar experimentally-determined ligand binding sites through an…

Identifies similar experimentally-determined ligand binding sites through an exhaustive pair-wise search of the RCSB PDB. CPASS is an integral component of the FAST-NMR methodology to annotate…

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.

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…

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…

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.…

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…

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…

SInCRe
Dataset

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…

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…

LigBase
Dataset

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.

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.

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…

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.…

CSAR
Dataset

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…

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…

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…

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.