Protein Protein Docking

• 3D-Garden: A system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm (online)
  
• AREA-AFFINITY: Server for Machine Learning-Based Prediction of Protein-Protein and Antibody-Protein Antigen Binding Affinities (online)
  
• Arpeggio: A webserver for calculating interatomic interactions in protein structures (online & standalone)
  
• BAlaS: fast, interactive and accessible computational alanine-scanning using BudeAlaScan (online)
  
• Cluspro: protein docking (online)
  
• ClusPro FMFT-SAXS: Ultra-fast Filtering Using Small-Angle X-ray Scattering Data in Protein Docking (online and standalone)
  
• ClusPro TBM: Toward combining template-based methods with free docking (protein-protein docking) (online)
  
• ClusPro-DC: discrimination between Xray and biological dimers (online requires login)
  
• CoDockPP: A Multistage Approach for Global and Site-Specific Protein-Protein Docking (online)
  
• DeepComplex: A Web Server of Predicting Protein Complex Structures by Deep Learning Inter-chain Contact Prediction and Distance-Based Modelling (online)
  
• DisVis: visualizes the accessible interaction space (online)
  
• DOCK/PIERR: Protein Docking Server (online)
  
• Dockground: A comprehensive data resource for modeling of protein complexes, datasets, decoys... (online)
  
• DOCKSCORE: rank docked poses (online)
  
• DockStar: Modelling of multimolecular protein complexes (online)
  
• DockSurf: A molecular modeling software for the prediction of protein/surface adhesion (eg. gold surfaces) (online)
  
• DOVE: convolutional deep neural network-based approach named DOcking decoy selection with Voxel-based deep neural nEtwork (DOVE) for evaluating protein docking models (online)
  
• EROS-DOCK: protein–protein docking using exhaustive branch-and-bound rotational search (standalone)
  
• ezCADD: a Rapid 2D/3D Visualization Enabled Web Modeling Environment for Democratizing Computer-Aided Drug Design (small molecule docking, protein docking, 2D/3D interaction viz, de novo lead optimization, pocket search and polypharmacology) online
  
• FiberDock, FireDock, FlexDock, PatchDock: FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking
  
• FiltRest3D: filter predicted models (online)
  
• FoldDock: simultaneous folding and docking protocol FoldDock and AlphaFold (standalone)
  
• FRODOCK: Fast Rotational DOCKing (online)
  
• GalaxyDomDock: An Ab Initio Domain-domain Docking Web Server for Multi-domain Protein Structure Prediction (online)
  
• GalaxyHomomer: protein homo-oligomer structure prediction from a monomer sequence or structure (online)
  
• GalaxyRefineComplex: Protein-protein complex structures generated by protein-protein docking methods can be refined (online)
  
• GalaxyTongDock: Symmetric and asymmetric ab initio protein-protein docking web server with improved energy parameters (online)
  
• GRAMM: Protein-Protein Docking Web Server (online)
  
• GraphPPIS: Structure-aware protein-protein interaction site prediction using deep graph convolutional network (online), standalone on github
  
• GWIDD: genome wide docking database (online)
  
• Haddock: High Ambiguity Driven protein-protein DOCKing (online requires login)
  
• HawkDock: to predict and analyze the protein-protein complex based on computational docking and MM/GBSA (online)
  
• HDOCK: hybrid protein–protein and protein–DNA/RNA docking, Pushing the accuracy limit of shape complementarity for protein-protein docking (online)
  
• HMI-PRED: A Web Server for Structural Prediction of Host-Microbe Interactions Based on Interface Mimicry (online)
  
• InterEvDock2: protein docking using evolutionary and biological information from homology models and multimeric inputs (online)
  
• InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps (online)
  
• InterPred: A pipeline to identify and model protein-protein interactions (online)
  
• INTERSPIA: Explore the Dynamics of Protein-Protein Interactions Among Multiple Species (online)
  
• IRaPPA: pyDockRescoring Server (online)
  
• LightDock: Artificial Intelligence-powered modeling of macromolecular interactions (macromolecular docking framework, online)
  
• P3DOCK: a protein-RNA docking webserver based on template-based and template-free docking (online)
  
• PIIMS: Mutation Hotspot Scanning at the Protein-Protein Interface (online)
  
• PPI-Affinity: Prediction and Optimization of Protein-Peptide and Protein-Protein Binding Affinity (online)
  
• PRODIGY: PROtein binDIng enerGY prediction (online)
  
• PRODIGY-crystal: classification of biological interfaces in protein complexes (online)
  
• pyDock: pyDockWEB: a web server for rigid-body protein–protein docking using electrostatics and desolvation scoring
  
• pyDockDNA: A new web server for energy-based protein-DNA docking and scoring (online)
  
• pyDockEneRes: per-residue decomposition of protein-protein docking energy (online)
  
• QASDOM: Quality ASsessment of DOcking Models, protein-protein (online)
  
• RosettaDock: Efficient Flexible Backbone Protein-Protein Docking for Challenging Targets (standalone and online)
  
• SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions (PPI) (online) (or http://sbi.upf.edu/spserver/)
  
• SwarmDock: webservice for generating 3D structures of protein-protein complexes (online)
  
• webSDA: Simulation of Diffusional Assosiation (SDA) (online)
  
• ZDOCK: docking (online)
  

Quality Assessment

• DockQ: A Quality Measure for Protein-Protein Docking Models (standalone)