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Protein-protein docking

Template-based docking

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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
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