Protein-protein docking and homology modeling of complexes

  • pyDock - Protein-protein docking (see below for online) - standalone
  • PrePPItar - Computational probing protein-protein interactions targeting small molecules - standalone
  • KSENIA - Knowledge of Native Protein-Protein Interfaces is Sufficient to Construct Predictive Models for the Selection of Binding Candidates (protein docking, knowledge-based potential) - standalone
  • MEPSA - Minimum energy pathway analysis for energy landscapes - standalone
  • PRODIGY - Binding affinity of protein-protein complexes - standalone
  • DOCKSCORE - A webserver for ranking protein-protein docked poses - online
  • Galaxy - GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking - online
  • HDOCK - hybrid protein–protein and protein–DNA/RNA docking (2017) - online
  • DisVis - Visualizes the accessible interaction space - online
  • DockStar - Modelling of multimolecular protein complexes - docking - online
  • FiltRest3D - Filtering protein models by fuzzy restraints. Discrimination of native-like complexes from low-resolutions docking decoys - online and standalone
  • InterEvDock - Docking server to predict the structure of protein–protein interactions using evolutionary information - online
  • MinkoFit3D - A swebserver for fitting macromolecular assemblies into low-resolution electron density maps using Minkowski sum analysis - online
  • (PS)2 - Prediction of protein complexes by comparative modeling(PS)2 - online
  • pyDock - pyDockSAXS: Protein protein complex structure by SAXS and computational docking - online
  • DockAFM - Docking structures under an AFM surface - online
  • webSDA - A web server to simulate macromolecular diffusional association - online
  • AIDA - Ab initio domain assembly for automated multi-domain protein structure prediction and domain–domain interaction prediction - standalone and online server
  • side chains - The Impact of Side-Chain Packing on Protein Docking Refinement - standalone
  • Docks - AFM - Combine of docking solutions of structural subunits under an AFM surface (2014). CombineDocksAFM - online
  • SPOT:RNA - SPOT-Seq-RNA: Predicting Protein-RNA Complex Structure and RNA-Binding Function by Fold Recognition and Binding Affinity Prediction - online
  • LoopFinder - A web-based interface for LoopFinder (predict loops at interfaces, could be used for cmpd design) is currently under construction. In the meantime, LoopFinder is freely available for use. Requests for binary files or code can be sent to This email address is being protected from spambots. You need JavaScript enabled to view it. (Gavenonis et al, Nat Chem Biol. 2014) - standalone for now
  • heparin - Heparin docking server for the identification of heparin binding sites on proteins (advanced option of the ClusPro server) - online
  • PPI - Scoring docking conformations using predicted protein interfaces: T-PIP (For Protein Interface Prediction) and T-PioDock (For Ranking Docking Models) software - standalone
  • DoBi - Find binding sites and can be used for docking - standalone
  • Cell-Dock - High-performance protein-protein docking - standalone
  • SEQMOL - Protein-protein docking: SEQMOL as a decoy filtering utility to select the best models - standalone
  • Kd server - CRYSTAL STRUCTURE Kd SERVER (with SEQMOL). PDB to free energy (Alexei Korennykh lab). The algorithm was trained using experimentally determined binding parameters from about a hundred of different complexes. The software measures dG from calculating dS and dH of the interfaces. The paper will be published in the coming months - check with the authors
  • Datasets - Complete Cross Docking Data Of Mintseris Benchmark 2.0 - dataset
  • InterPreTS - Interaction Prediction through Tertiary Structure: Given a set of protein sequences (in fasta format), this tool will use BLAST to find homologues of known structure for all pairs (i.e. templates that can model each pair of sequences based on homology) and then evaluate the suitability of those templates for modelling the interaction. Template-based docking - standalone
  • Struct2Net - Struct2Net or Coev2Net Predict PPIs by combining a structure-based threading approach with machine learning techniques. Also compute a confidence score that addresses both false-positive and false-negative rates. Template-based docking - online
  • Interact. - Interactome3D: a web service for the structural annotation of protein-protein interaction networks - online
  • KBDOCK - KBDOCK (knowledge-based protein docking, docking under restraints) - database and online
  • FunHunt - FunHunt is a classifier of correct protein-protein complex orientations. The input to FunHunt are two possible orientations of a complex. A local docking run is performed on the two complexes using RosettaDock. FunHunt then uses features gathered from these docking runs - representing the local energy landscapes of the orientations, and chooses the near-native orientation among both (assuming that one of the orientations is the near native one) - online
  • F2Dock - F2Dock, a rigid-body protein-protein docking software - online upon request
  • BiGGER - Chemera is a molecular modelling and graphics application that also serves as the interface to BiGGER (protein-protein docking) - standalone
  • FiberDock - Flexible Induced-fit Backbone Refinement in Molecular Docking. FiberDock is an efficient method for flexible refinement and re-scoring of rigid-body protein-protein docking solutions - online
  • FRODOCK - Fast Rotational DOCKing. Generates very efficiently many potential predictions of how two proteins could interact - online
  • DOCK - DOCK/PIE(RR): Web Server for Structure Prediction of Protein-Protein Complexes - online
  • ZDOCK - ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers - online
  • dDFIRE / DFIRE2 - Energy calculation - online
  • PRISM - PRotein Interactions by Structural Matching - online
  • DIMER - PREDDIMER: a web server for prediction of transmembrane helical dimers - online
  • SPRING - SPRING is a template-base algorithm for protein-protein structure prediction - online
  • COTH - COTH (CO-THreader) is a multiple-chain protein threading algorithm which is designed to identify and recombine protein complex structures from both tertiary and complex structure libraries - online
  • TACOS - TACOS (Template-based Assembly of Complex Structures) is designed to model the structure of protein-protein complexes based on a hierarchical approach of template identification and structural refinement - online
  • HOMCOS - HOmology Modeling of protein COmplex Structure - online
  • Udock - The Interactive Docking Entertainment System - standalone (windows)
  • DockTrina - Docking triangular protein trimers - docking, standalone
  • DockRank - Ranking docked conformations using partner-specific sequence homology based protein interface prediction - online scoring
  • MEGADOCK - An All-to-all Protein-protein Interaction Prediction System Using Tertiary Structure Data. Last version is 4, June 2014 - PPI docking, standalone
  • Score-MI - An information-theoretic classification of amino acids for the assessment of interfaces in protein-protein docking. The reduced alphabets derived from the present work were converted into a scoring function for the evaluation of docking solutions, which is available for public use via the web service score-MI - online scoring
  • SymmDock - Prediction of Complexes with Cn Symmetry by Geometry Based Docking - online
  • LZerD - Protein-Protein Docking Algorithm - standalone
  • PI-LZerD - Protein Docking Prediction Using Predicted Protein-Protein Interface - standalone
  • F(2)Dock 2.0 - Protein-Protein Docking with F(2)Dock 2.0 and GB-Rerank - PPI docking, online site 1
  • F(2)Dock 2.0 - Protein-Protein Docking with F(2)Dock 2.0 and GB-Rerank - PPI docking, online site 2
  • Link - PTools : a C++ and Python library for macromolecular docking - standalone
  • ATTRACT - Docking Program (Fortran-Version, full source code and manual) - standalone
  • SwarmDock - A server for flexible protein-protein docking - online docking
  • Link - Prune and Probe: Two modular web services for protein-protein docking - docking online
  • 3D-GARDEN - Global and Restrained Docking Exploration Nexus 3D-GARDEN is a state-of-the-art comprehensive software suite and server for protein-protein docking with full high-performance computing functionality - online docking
  • Database - DOCKGROUND: The resource implements a comprehensive database of co-crystallized (bound-bound) protein-protein complexes - Database of experimental complexes
  • FireDock - The server addresses the refinement problem of protein-protein docking solutions - Macromolecular docking online
  • Grammx - Tools for protein-protein docking. GrammX: web interface of Gramm - Macromolecular docking online, see also standalone
  • LIGIN - Molecular docking using surface complementarity. The LIGIN program is also available as part of WHATIF -  standalone
  • PatchDock - Protein docking tools (PatchDock) and related. PatchDock, webserver for macromolecules and small molecules docking based on shape complementarity criteria. There are many other tools here including tools for peptides, flexibility, comparing binding pockets... - online docking
  • AquaSAXS - A web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models - online
  • PBSword -  A web server designed for efficient and accurate comparisons and searches of geometrically similar protein-protein binding sites from a large-scale database - online
  • InterEvScore - A novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution - standalone
  • pyDockWEB - A web server that returns the best rigid-body docking orientations generated by FTDock and evaluated by pyDock scoring function, which includes electrostatics, desolvation energy and limited van der Waals contribution - online
  • PyDock - Tool for protein-protein docking. The module ODA can help to predict potential protein-protein interaction regions. pyDock is a fast protocol which uses electrostatics and desolvation energy to score docking poses generated with FFT-based algorithms - standalone
  • HINT - HINT (High-quality INTeractomes) is a database of high-quality protein-protein interactions in different organisms - database
  • HADDOCK - Docking driven by interface restraints - online
  • SmoothDock - Protein docking - docking online
  • Bipdock - Bielefeld Protein Docking Software - standalone
  • ZDOCK - docking based on FFT search - standalone
  • ClusPro - Protein-protein docking webserver using 3 docking programs - DOT ZDOCK GRAMM - docking online
  • PIC - Protein Interactions Calculator - online
  • DOT - Protein-protein docking software -  standalone
  • ROSIE - ROSIE, including rosetta Protein-protein docking -  online
  • CombDock - Combinatorial assembly of multiprotein complexes by multiple docking (see also Firedock) -  standalone
  • RosettaDock - The RosettaDock server - docking
  • BDOCK - Protein-protein docking software integrating the degree of burial of surface residues into protein-protein docking -  standalone
  • Hex -  Protein-protein docking and molecular superposition program - docking online
  • ESCHER-NG - Protein-protein and DNA-protein docking software - standalone
  • FTDock -  Fourier Transform Dock -  standalone
  • FastContact - : a free energy scoring tool for protein protein complex structures (PPI) - Scoring (PPI) online
  • ADP_EM - Makes it possible to accurately dock atomic structures into low-resolution electron-density maps -  standalone
  • PARE - The program PARE calculates the change in rate of association (kon) of mutant protein-protein interaction complexes from the change in the Debye Huckel energy of interaction - Structural Analysis, binding, mutations, online
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