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

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…

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…

webSDA
Web

webSDA

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

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…

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…

DOCK/PIERR
Web

DOCK/PIERR

A protein-protein docking algorithm based on residue contact potential PIE and…

A protein-protein docking algorithm based on residue contact potential PIE and atomic potential PISA. DOCK/PIERR predicts the quaternary structure of the complex formed by two proteins, given their…

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…

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…

PPI4DOCK
Data

PPI4DOCK

A large benchmark set for studying protein docking/scoring methods. PPI4DOCK…

A large benchmark set for studying protein docking/scoring methods. PPI4DOCK contains 1417 non-redundant docking targets between two subunits. Each subunit is a protein model obtained by homology…

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…

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…

AnkPlex
Web

AnkPlex

A web application developed to easily dicide the near-native docking complexes…

A web application developed to easily dicide the near-native docking complexes (poses) of ankyrin and their protein generated by ZDOCK program. The scoring features of docking poses are performed on…

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…

NOXclass
Desktop
Web

NOXclass

A classifier identifying protein-protein interaction types (biological…

A classifier identifying protein-protein interaction types (biological obligate, biological non-obligate and crystal packing) implemented using a support vector machine (SVM) algorithm. NOXclass…

DOCKGROUND
Data

DOCKGROUND

Provides data to improve our understanding of protein–protein interactions…

Provides data to improve our understanding of protein–protein interactions and to assist in the development of better tools for structural modeling of protein complexes, such as docking algorithms…

cNMA
Desktop

cNMA complex-based Normal Mode Analysis

Provides tools for dimensionality reduction of conformational space in flexible…

Provides tools for dimensionality reduction of conformational space in flexible protein docking. cNMA focuses on improving conformational representation thus is assessed in a critical way using…

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…

Multi-LZerD
Desktop

Multi-LZerD

A computational multiple protein docking algorithm that builds models of…

A computational multiple protein docking algorithm that builds models of multimeric complexes by effectively reusing pairwise docking predictions of component proteins. A genetic algorithm is applied…

FTDock
Desktop

FTDock Fourier Transform rigid-body Docking

Discretises two molecules onto orthogonal grids and performs a global scan of…

Discretises two molecules onto orthogonal grids and performs a global scan of translational and rotational space. In order to scan rotational space it is necessary to rediscretise one of the…

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,…

MM-ISMSA
Desktop

MM-ISMSA

An ultrafast and accurate scoring function for protein-protein docking. It…

An ultrafast and accurate scoring function for protein-protein docking. It includes (1) a molecular mechanics (MM) part based on a 12–6 Lennard-Jones potential; (2) an electrostatic component based…

COCOMAPS
Web

COCOMAPS bioCOmplexes COntact MAPS

A web application to easily and effectively analyse and visualize the interface…

A web application to easily and effectively analyse and visualize the interface in biological complexes (such as protein-protein, protein-DNA and protein-RNA complexes), by making use of…

CONS-COCOMAPS
Web

CONS-COCOMAPS CONSensun COCOMAPS

A tool to easily measure and visualize the consensus in multiple docking…

A tool to easily measure and visualize the consensus in multiple docking solutions. It uses the conservation of inter-residue contacts as an estimate of the similarity between different docking…

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…

Complex Portal
Data

Complex Portal

A manually curated, encyclopaedic resource of macromolecular complexes from a…

A manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms. All data is freely available for search and download. The Complex Portal is hosted by the…

CCharPPI
Web
PyRosetta
Desktop

PyRosetta

An interactive Python-based interface to the powerful Rosetta molecular…

An interactive Python-based interface to the powerful Rosetta molecular modeling suite.

SKEMPI
Data

SKEMPI

Contains data on the changes in thermodynamic parameters and kinetic rate…

Contains data on the changes in thermodynamic parameters and kinetic rate constants upon mutation, for protein-protein interactions for which a structure of the complex has been solved and is…

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.

Cell-Dock
Desktop

Cell-Dock

A FFT-based docking method optimized for the Cell BE processor.

A FFT-based docking method optimized for the Cell BE processor.

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.

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…

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…

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.

pyDockWEB
Web

pyDockWEB

A web server for the structural prediction of protein-protein interactions.

A web server for the structural prediction of protein-protein interactions.

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.

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.

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.

RosettaDock
Web

RosettaDock

Identifies low-energy conformations of a protein-protein interaction near a…

Identifies low-energy conformations of a protein-protein interaction near a given starting configuration by optimizing rigid-body orientation and side-chain conformations.

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.

Cluspro
Web

Cluspro

Web-based program for the computational docking of protein structures.

Web-based program for the computational docking of protein structures.

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.

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.

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