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Protein-protein docking tools

Protein-protein interactions lie at the heart of most cellular processes. Protein-protein docking is important for understanding disease mechanisms and for drug discovery.

HADDOCK
Web

HADDOCK High Ambiguity Driven protein-protein DOCKing

An information-driven flexible docking approach for the modeling of…

An information-driven flexible docking approach for the modeling of biomolecular complexes. HADDOCK distinguishes itself from ab-initio docking methods in the fact that it encodes information from…

PatchDock
Web
Desktop

PatchDock

Finds docking transformations that yield good molecular shape complementarity.…

Finds docking transformations that yield good molecular shape complementarity. A wide interface is ensured to include several matched local features of the docked molecules. PatchDock divides the…

KBDOCK
Dataset

KBDOCK

Defines and spatially clusters protein binding sites for knowledge-based…

Defines and spatially clusters protein binding sites for knowledge-based protein docking. KBDOCK is a 3D database system that combines the PFAM domain classification with coordinate data from the…

Cluspro
Web

Cluspro

Predicts protein–protein interactions (PPIs). Cluspro is an automated web…

Predicts protein–protein interactions (PPIs). Cluspro is an automated web server for protein-protein docking. The software can discriminate putative structures generated by the user, executing any…

RosettaDock
Server

RosettaDock

Assists in finding a minimum free-energy complex structure. RosettaDock is a…

Assists in finding a minimum free-energy complex structure. RosettaDock is a multi-start, multi-scale Monte Carlo based algorithm which searches the rigid-body and side-chain conformational space of…

pyDock
Web
Desktop

pyDock

Allows structural prediction of protein-protein interactions (PPIs). pyDock is…

Allows structural prediction of protein-protein interactions (PPIs). pyDock is a docking protocol scoring docking poses generated with FFT-based algorithms. The software contains the pyDockNIP module…

PRODIGY
Web

PRODIGY PROtein binDIng enerGY prediction

A web server to predict the binding affinity of protein-protein complexes from…

A web server to predict the binding affinity of protein-protein complexes from their three-dimensional structure. The PRODIGY server implements our simple but highly effective predictive model based…

GRAMM-X
Web

GRAMM-X

Extend the original GRAMM Fast Fourier Transformation methodology by employing…

Extend the original GRAMM Fast Fourier Transformation methodology by employing smoothed potentials, refinement stage, and knowledge-based scoring.

FireDock
Web

FireDock

An efficient method for refinement and re-scoring of rigid-body protein-protein…

An efficient method for refinement and re-scoring of rigid-body protein-protein docking solutions.

ZDOCK
Web

ZDOCK

A user-friendly protein docking server, based on the rigid-body docking…

A user-friendly protein docking server, based on the rigid-body docking programs ZDOCK and M-ZDOCK, to predict structures of protein-protein complexes and symmetric multimers.

HexServer
Web

HexServer

Fourier transform (FFT)-based protein docking server to be powered by graphics…

Fourier transform (FFT)-based protein docking server to be powered by graphics processors.

FRODOCK
Desktop

FRODOCK Fast Rotational DOCKing

A user-friendly protein-protein docking server based on an improved version of…

A user-friendly protein-protein docking server based on an improved version of FRODOCK that includes a complementary knowledge-based potential. The web interface provides a very effective tool to…

FunHunt
Web

FunHunt

Corrects protein-protein complex orientations. FunHunt is also able to choose…

Corrects protein-protein complex orientations. FunHunt is also able to choose the near-native orientation among models created by algorithms other than RosettaDock, demonstrating its general…

webSDA
Web

webSDA

Calculates bimolecular protein–protein association rate constants. SDA has been…

Calculates bimolecular protein–protein association rate constants. SDA has been extended to study electron transfer rates, to predict the structures of biomacromolecular complexes, to investigate the…

Homology…
Dataset

Homology Docking Benchmark

Assists users in exploring and solving combined modeling and docking problems.…

Assists users in exploring and solving combined modeling and docking problems. Homology Docking Benchmark provides means to generate large, customized ensembles of potential template structures from…

FiberDock
Web

FiberDock

An efficient method for flexible refinement and re-scoring of rigid-body…

An efficient method for flexible refinement and re-scoring of rigid-body protein-protein docking solutions.

InterEvDock
Web

InterEvDock

A server for protein docking based on a free rigid-body docking strategy. It…

A server for protein docking based on a free rigid-body docking strategy. It relies on the integration of various components for decoy generation and scoring. Particularly, the combination of the…

PIPER
Desktop

PIPER

Generates accurate structures of protein-protein complexes. PIPER is a Fast…

Generates accurate structures of protein-protein complexes. PIPER is a Fast Fourier Transform (FFT)-based protein docking program, extended to be used with pairwise interaction potentials and based…

3DIANA
Web
Desktop

3DIANA 3D Domain Interaction Analysis

A web based environment designed to integrate bioinformatics-like information…

A web based environment designed to integrate bioinformatics-like information for the analysis of protein interactions and quaternary structure modellling. 3DIANA is specially targeted to the cases…

PEPSI-Dock
Desktop

PEPSI-Dock Polynomial Expansion of Protein Structures and Interactions for Docking

Combines a distant-dependent knowledge-based potential with Fast Fourier…

Combines a distant-dependent knowledge-based potential with Fast Fourier Transform (FFT)-accelerated exhaustive sampling on spherical grids. Our potential approximates the binding free energy of…

SwarmDock
Web

SwarmDock

A web server that wraps and extends the SwarmDock flexible protein-protein…

A web server that wraps and extends the SwarmDock flexible protein-protein docking algorithm.

ProQDock
Desktop

ProQDock

A scoring function that predicts the absolute quality of docking model measured…

A scoring function that predicts the absolute quality of docking model measured by a novel protein docking quality score (DockQ). ProQDock uses support vector machines trained to predict the quality…

3D-Garden
Web

3D-Garden

Their benchmarked and server-ready flexible docking system, allows…

Their benchmarked and server-ready flexible docking system, allows sophisticated programming of surface patches by the user via a facet representation of the interactors' molecular surfaces.

InterEvScore
Desktop

InterEvScore

Provides each residue with the opportunity to contribute in its most favorable…

Provides each residue with the opportunity to contribute in its most favorable local structural environment. InterEvScore is a scoring function using a coarse-grained statistical potential including…

DOT
Desktop

DOT

A software package for docking macromolecules, including proteins, DNA, and RNA.

A software package for docking macromolecules, including proteins, DNA, and RNA.

CPdock
Desktop

CPdock Complementarity Plot

Calculates shape and electrostatic complementarities for amino acid side-chains…

Calculates shape and electrostatic complementarities for amino acid side-chains buried within the protein interior. CPdock is an established graphical structure validation tool in the field of…

LightDock
Desktop

LightDock

Allows protein-protein docking. LightDock is based on the Glowworm Swarm…

Allows protein-protein docking. LightDock is based on the Glowworm Swarm Optimization (GSO) algorithm for sampling the translational and rotational space of protein-protein docking, and anisotropic…

Kinase Crystal…
Desktop

Kinase Crystal Miner

Intends to identify the hinge binding motif of a ligand in a ligand-protein…

Intends to identify the hinge binding motif of a ligand in a ligand-protein co-crystal structure. Kinase Crystal Miner permits to identify the hinge binding motif and the associated attachment…

HDOCK
Web

HDOCK

Provides a user-friendly web access to a hybrid algorithm of template-based…

Provides a user-friendly web access to a hybrid algorithm of template-based modeling and free docking for protein-protein and protein-DNA/RNA complexes. HDOCK is a docking server that efficiently…

ClusPro…
Web

ClusPro PeptiDock

Uses an approach for the efficient docking of peptide motifs to their free…

Uses an approach for the efficient docking of peptide motifs to their free receptor structures. Using a motif based search, ClusPro PeptiDock can retrieve structural fragments from the Protein Data…

AnkPlex
Web

AnkPlex

Aims users to predict near-native states of ankyrin-protein complexes. AnkPlex…

Aims users to predict near-native states of ankyrin-protein complexes. AnkPlex allows users to: (1) analyze and characterize ankyrin-protein complexes by using a set of informative features that have…

InteractiveROSE…
Desktop

InteractiveROSETTA

A graphical interface for the PyRosetta framework that presents easy-to-use…

A graphical interface for the PyRosetta framework that presents easy-to-use controls for several of the most widely-used Rosetta protocols alongside a sophisticated selection system utilizing PyMOL…

cNMA
Desktop

cNMA complex-based Normal Mode Analysis

Provides a dimensionality reduction of conformational space in flexible protein…

Provides a dimensionality reduction of conformational space in flexible protein docking. cNMA determines weights or coefficients for individual modes, and increases protein docking results. It can…

DockStar
Web

DockStar

An algorithm for modeling of multimolecular protein complexes. DockStar…

An algorithm for modeling of multimolecular protein complexes. DockStar integrates both high resolution data of the individual subunits and low resolution data, such as the complex interaction graph…

CONSRANK
Web

CONSRANK CONSensus-RANKing

A web tool for analyzing, comparing and ranking protein-protein and…

A web tool for analyzing, comparing and ranking protein-protein and protein-nucleic acid docking models, based on the conservation of inter-residue contacts and its visualization in 2D and 3D…

CCharPPI
Web
DockTrina
Desktop

DockTrina

Scans all possible combinations of contacts between three monomers, with the…

Scans all possible combinations of contacts between three monomers, with the total number of about 1010 combinations. DockTrina is a protein docking method for modeling the 3D structures of…

ProPairs
Dataset

ProPairs

Contains crystal structures of protein complexes defined as biological…

Contains crystal structures of protein complexes defined as biological assemblies in the protein data bank (PDB). ProPairs has identified 5,642 protein complexes with 11,600 different decompositions…

DoBi
Desktop

DoBi

Predicts the binding sites on pair of given proteins. DoBi is a Java software…

Predicts the binding sites on pair of given proteins. DoBi is a Java software that need to type a command line. Four arguments are required: (i) the PDB code of a protein chain, (ii) the PDB code of…

V-D2OCK
Web

V-D2OCK VORFFIP-driven dock

A computational strategy to predict the structure of protein complexes based on…

A computational strategy to predict the structure of protein complexes based on data-driven docking. V-D²OCK has been benchmarked using a validated and diverse set of protein complexes and compared…

ATTRACT
Web
Desktop

ATTRACT

Allows users to predict complex structures. ATTRACT is a program available…

Allows users to predict complex structures. ATTRACT is a program available through a desktop version and a web application. It can tackle a large variety of docking problems, due to an extensive set…

ClusPro-DC
Web

ClusPro-DC

Implements a straightforward approach to the discrimination between…

Implements a straightforward approach to the discrimination between crystallographic and biological dimers by docking the two subunits to exhaustively sample the interaction energy landscape.…

PRUNE
Web

PRUNE

Selects a subset of docking poses generated during sampling search. PRUNE uses…

Selects a subset of docking poses generated during sampling search. PRUNE uses a single parameter, interface-area-based edge function that has been shown to time-efficiently select subsets of docking…

MEGADOCK
Desktop

MEGADOCK

A structural bioinformatics software for FFT-grid-based protein-protein docking…

A structural bioinformatics software for FFT-grid-based protein-protein docking that takes advantage of the massively parallel CUDA architechture of NVIDIA GPUs and multiple computation nodes.

PPA-Pred
Web

PPA-Pred Protein-Protein Affinity Predictor

This server helps you in predicting the binding affinity of protein-protein…

This server helps you in predicting the binding affinity of protein-protein complex of your interest.

DockRank
Web

DockRank

A tool to rank protein-protein docked models based on predicted…

A tool to rank protein-protein docked models based on predicted partner-specific protein interface residues. DockRank uses PS-HomPPI to predict the partner-specific protein interface residues for the…

DOCKSCORE
Desktop
Web

DOCKSCORE

An objective scoring scheme that can be used to rank protein-protein docked…

An objective scoring scheme that can be used to rank protein-protein docked poses. DOCKSCORE considers several interface parameters, namely, surface area, evolutionary conservation, hydrophobicity,…

F2Dock
Desktop

F2Dock Fast Fourier Protein-Protein Docking

A package for rigid-body protein-protein docking. F2Dock is based on an…

A package for rigid-body protein-protein docking. F2Dock is based on an extensive experimental study on a list of benchmark complexes. The method is structured to incorporate Lennard-Jones potential…

Udock
Desktop

Udock

Allows a quick and easy-to-handle human driven exploration of protein–protein…

Allows a quick and easy-to-handle human driven exploration of protein–protein interfaces. Udock is an interactive protein docking system that makes use of users' cognitive capabilities added up.…

Seqmol
Desktop

Seqmol Sequences and molecules

Identifies stable or weak complexes by calculating Kd for formation of…

Identifies stable or weak complexes by calculating Kd for formation of interfaces. SEQMOL is a protein data bank (PDB) structure analysis suite. It can be used to align multiple protein and DNA…

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