Last update:   October 9, 2011
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Reviews and fundamental papers
Prediction contest CAPRI
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Protein-protein (peptide) docking
Protein-ligand docking
Protein-protein and protein ligand docking
Related programs for analysis and visualization
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Books Other information
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Reviews and fundamental papers
Archakov, A.I.; Govorun, V.M.; Dubanov, A.V.; Ivanov, Y.D.; Veselovsky, A.V.; Lewi, P.; Janssen, P.; Proteomics 2003, 3(4), 380-391. Protein-protein interactions as a target for drugs in proteomics.
Halperin, I.; Ma, B.; Wolfson, H.; Nussinov, R.; Proteins 2002, 47(4), 409-443. Principles of docking: an overview of search algorithms and a guide to scoring functions.
Mendez, R.; Leplae, R.; De Maria, L.; Wodak, S.J.; Proteins 2003, 52(1), 51-67. Assessment of blind predictions of protein-protein interactions: current status of docking methods.
Vajda, S.; Camacho, C.J.; Trends Biotechnol. 2004, 22(3), 110-116. Protein-protein docking: is the glass half-full or half-empty?
Xenarios, I.; Eisenberg, D.; Curr. Opin. Biotechnol. 2001, 12(4), 334-339. Protein interaction databases.  

Prediction contest CAPRI
CAPRI - Critical Assessment of PRedicted Interactions
Meeting report 2001: Modeling of protein interactions in genomes  
Janin, J.; Henrick, K.; Moult, J.; Eyck, L.T.; Sternberg, M.J.; Vajda, S.; Vakser, I.; Wodak, S.J.; Proteins 2003, 52(1), 2-9. CAPRI: a critical assessment of predicted interactions.
Janin, J.; Protein Sci. 2005, 14(2), 278-283. Assessing predictions of protein-protein interaction: the CAPRI experiment.
Janin, J.; Proteins 2007, 69(4), 699-703. The targets of CAPRI rounds 6-12.
Janin, J.; Wodak, S.; Structure 2007, 15(7), 755-759. The third CAPRI assessment meeting Toronto, Canada, April 20-21, 2007.
Lensink, M.F.; Méndez, R.; Wodak, S.J.; Proteins 2007, 69(4), 704-718. Docking and scoring protein complexes: CAPRI 3rd eEdition.


Protein-protein (peptide) docking

3D-Dock Suite (BioMolecular Modeling, Cancer Research UK)
  • FTDock, RPScore and MultiDock
3D-Garden (Imperial College London)
  • Global And Restrained Docking Exploration Nexus
  • system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm
Bielefeld Protein Docking (Bielefeld University)
  • detects geometrical and chemical complementarities between surfaces of proteins and estimates docking positions
BiGGER (BioTecnol, S.A.)
  • protein-docking algorithm; intergrated in chemera, a molecular graphics and modeling program for studying protein structures and interactions
ClusPro (Boston University)
  • integrated approach to protein-protein docking; DOT and ZDOCK
DOT (San Diego Supercomputer Center)
  • Daughter Of Turnip
  • computation of the electrostatic potential energy between two proteins or other charged molecules
ESCHER NG (Milan University)
  • enhanced version of the original ESCHER protein-protein automatic docking system developed in 1997
FireDock (Tel Aviv University & Center for Cancer Research Nanobiology Program)
  • Fast Interaction REfinement in molecular DOCKing
  • web server for flexible refinement and scoring of protein-protein docking solutions
  • includes optimization of side-chain conformations and rigid-body orientation and allows a high-throughput refinement
HADDOCK (Utrecht University Netherlands)
  • High Ambiguity Driven protein-protein DOCKing
HEX (University of Aberdeen)
  • protein docking and molecular superposition program
RosettaDock Server (Johns Hopkins University)
  • predicts the structure of protein complexes given the structures of the individual components and an approximate binding orientation


Protein-ligand docking

Affinity (Accelrys Inc.)
AutoDock (The Scripps Research Institute)
CombiBUILD (Sandia National Labs)
  • fragment-based docking; program created to aid the design of combinatorial libraries
DockVision (University of Alberta)
eHiTS (SimBioSys Inc.)
  • electronic High Throughput Screening
  • fast, flexible docking of whole or partial structures to target receptors
FRED (OpenEye)
  • Fast Rigid Exhaustive Docking
  • multiconformer docking program
FlexiDock (Tripos)
FlexX (BioSolveIT GmbH)
GLIDE (Schrödinger GmbH)
HINT (Virginia Commonwealth University)
  • Hydropathic INTeractions
LIGPLOT (University College of London)
  • program for automatically plotting protein-ligand interactions
POCASA (Graduate School of Life Science)
  • POcket-CAvity Search Application
  • predict binding sites by detecting pockets and cavities of proteins of known 3D structure
Pocket- Finder (University of Leeds)
  • pocket detection
Q-SiteFinder (University of Leeds)
  • ligand binding site prediction
QUANTUM (Quantum Pharmaceuticals)
  • binding affinity calculation based on quantum mechanics and statistical physics methods
SITUS (Scripps Research Institute)
  • program package for modeling of atomic resolution structures into low-resolution density maps
VEGA (Milan University)
  • calculation of ligand-receptor interaction energy


Protein-protein and protein ligand docking

DOCK (UCSF Molecular Design Institute) 
  • Global RAnge Molecular Matching
  • see also the database of Protein-Protein Decoys for the validation of energy functions and refinement procedures
ICM-Docking (MolSoft LLC) 
PatchDock (Tel Aviv University)
  • molecular docking algorithm based on shape complementarity principles


Related programs for analysis and visualization

aiSee (AbsInt Angewandte Informatik GmbH)
  • commercial graph layout software
APID (Cancer Research Center)
  • Agile Protein Interaction DataAnalyzer
  • interactive web-tool
  • all known experimentally validated protein-protein interactions
APID2NET (Cancer Research Center)
  • unified interactome graphic analyzer
  • open access tool, included in Cytoscape, that allows to surf unified interactome data by quering APID server and facilitates dynamic analysis of the protein-protein interaction (PPI) networks
  • visualize, dynamically explore and analyze the proteins and interactions retrieved, including all the annotations and attributes associated to such PPIs, i.e.: GO terms, Pfam and InterPro domains, experimental methods that validate each interaction, PubMed IDs, UniProt IDs, etc
AVIS (Mount Sinai School of Medicine)
  • AJAX Viewer of Interactive Signaling networks
  • Google gadget compatible web-based viewer of interactive cell signaling networks
BioJAKE (BIC Singapore)
  • Java program; tool for creation, visualization and manipulation of metabolic pathways [PDF]
BIOSMILE (National Tsing-Hua University & Yuan Ze University)
  • web-based NCBI-PubMed search application, which can analyze articles for selected biomedical verbs and give users relational information, such as subject, object, location, manner, time, etc.
Bioverse (University of Washington)
  • Java applet interface for visualizing interactomes
COCOMAPS (University of Salerno & University of Napoli 'Parthenope' )
  • bioCOmplexes COntact MAPS
  • 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 intermolecular contact maps
Cytoscape (Institute for Systems Biology & Whitehead Institute for Biomedical Research)
  • visualizing molecular interaction networks
dockYard (Indian Institute of Science)
  • repository of protein-protein docking decoys
Drugscore-PPI (Heinrich-Heine-University)
  • knowledge-based scoring function for computational alanine-scanning in protein-protein interfaces
  • dedicated to successfully identify hot spots in protein-protein interfaces
Dynamic Signaling Maps™ (Hippron Physiomics)
  • web-based software
EXpanda (Keio University)
  • Integrated platform for network analysis and visualization
  • Perl library which gives full-automatic connections to various biological databases
  • can perform topological analysis based on graph theory
GenoMax™ (Informax)
  • protein-protein interaction analysis module
GRAMM-X (University of Kansas)
  • protein docking web server
Graphviz (AT&T Research)
  • graph visualization software
HARMONY (The Scripps Research Institute)
  • spherical harmonic representations of molecular surfaces
HotDock (University Paderborn)
  • interactive approach to molecular docking
I2I-SiteEngine (Tel Aviv University)
  • Interface-to-Interface-SiteEngine
  • structural and physico-chemical alignment of protein-protein interfaces
iMolTalk (Swiss Institute of Bioinformatics)
  • identify protein-protein interfaces between chains in a structure
Integrator (University of Washington School of Medicine)
  • collection of interactive, graphical search tools for exploring protein-protein interaction networks
InteroPorc (IBITECS)
  • automatic prediction tool to infer protein-protein interaction networks
  • applicable for lots of species using orthology and known interactions
InterProSurf (University of Texas Medical Branch)
  • web server for predicting the functional sites on the protein surface
  • predicts interacting amino acid residues in proteins that are most likely to interact with other proteins
InterViewer (Inha University, WI Lab)
  • visualization and analysis of protein-protein interactions
iPfam (Sanger Institute)
  • visualization of protein-protein interactions at domains and amino acid resolutions
iVici (Universite de Montreal, Canada)
  • Interrelational Visualization and Correlation Interface
  • analyze cellular networks represented as addressable symmetric or asymmetric two-dimensional matrices
  • permit simultaneous visualization and correlation of multiple datasets, representing any relationship between a set of genes, mRNAs, or proteins
  • visual overlay of datasets and addressable access to gene annotations permits comparison of networks of different types (for example protein-protein interactions and genetic networks) or investigation of the dynamic reorganization of a particular network
Java 3D – MPI (University Georgia)
  • Java 3D - Mobile of Protein Interactions
jSquid (Stockholm University)
  • graph visualization tool for exploring graphs from protein-protein interaction or functional coupling networks
KFC Server (University of Wisconsin-Madison)
  • Knowledge-based Fade and Contacts
  • predicts binding "hot spots" within protein-protein interfaces by recognizing structural features indicative of important binding contacts
  • analyzes several chemical and physical features surrounding an interface residue and predicts the classification of the residue using a model trained on prior experimental data
MaGnET (University of Edinburgh)
  • Malaria GeNome Exploration Tool
  • LaCount, D.J.; Vignali, M.; Chettier, R.; Phansalkar, A.; Bell, R.; Hesselberth, J.R.; Schoenfeld, L.W.; Ota, I.; Sahasrabudhe, S.; Kurschner, C.; Fields, S.; Hughes, R.E. Nature 2005, 438(7064), 103-107. A protein interaction network of the malaria parasite Plasmodium falciparum. [PubMed]
metaPocket (EML Research gGmbH)
  • meta server to identify pockets on protein surface to predict ligand-binding sites
MidasPlus (UCSF, Computer Graphics Lab)
  • including the Viewdock tool for analyzing of DOCK output files
Moksiskaan (University of Helsinki)
  • computational platform that integrates pathway, protein-protein interaction, genome and literature mining data to result in comprehensive networks for a list of genes or proteins
MolSurfer (EML Research gGmbH Heidelberg)
  • macromolecular interface navigator
  • Java based software tool; 2D protein-protein interface maps to navigate 3D structures of proteins [PDF]
  • Gabdoulline, R.R.; Wade, R.C.; Walther, D.; Nucleic Acids Res. 2003, 31(13), 3349-3351. MolSurfer: a macromolecular interface navigator. [PubMed]
NAViGaTOR (University of Toronto)
  • Network Analysis, Visualization, & Graphing TORonto
  • software package for visualizing and analyzing protein-protein interaction networks
Osprey (Samuel Lunenfeld Research Institute)
  • network visualization system
PathDB™ (NCGR)
  • functional prototype research tool for biochemistry and functional genomics
  • tools for building, visualizing and comparing metabolic networks [Demo]
PathwayAssist™ (Ariadne Genomics)
  • cutting-edge software tool for visualization and interpretation of biological pathways, gene regulation networks and protein-protein interaction maps
PIANA (Structural Bioinformatics Group (GRIB-IMIM), Universitat Pompeu Fabra)
  • Protein Interactions And Network Analysis
  • software framework that facilitates the work with protein interaction networks by 1) integrating data from multiple sources in a centralized database, 2) providing a library that handles all operations related with the network and 3) automating the analysis of protein-protein interactions networks.
PIE (Seoul National University & National Institute of Standards and Technology)
  • Protein Interaction information Extraction system
  • online prediction system for protein-protein interactions from text
PIMRider® (Hybrigenics)
  • functional proteomics software platform; includes
    • PIM® - displays proteins in their respective networks
    • PBS® - filtering of interactions based on their reliability
    • SID® - identifies a specific protein domain involved in a given interaction [Guided Tour]
PIPSA (EML Research gGmbH Heidelberg)
  • Protein Interaction Property Similarity Analysis
  • compute and analyze the pairwise similarity of 3D interaction property fields for a set of proteins
  • produce a matrix of pairwise similarity indices for each protein interaction property; this matrix is converted into a distance matrix which may be used for clustering or visualization
PI-SCOUT™ (LION biosience)
  • visualizes and analyzes large molecular networks in interactive graphs [PDF]
Plasmodium falciparum Protein-Protein Interaction Network (Princeton University)
  • visualization of a protein-protein interaction dataset for Plasmodium falciparum, the bacterium responsible for malaria
PolySearch (University of Alberta)
  • supports >50 different classes of queries against nearly a dozen different types of text, scientific abstract or bioinformatic databases
  • exploits a variety of techniques in text mining and information retrieval to identify, highlight and rank informative abstracts, paragraphs or sentences
POLYVIEW-3D (University of Cincinnati)
  • generates animated images as well as publication quality static slides of protein 3D structures using the PDB formatted data
  • tool for protein structure analysis, with the focus on annotation and visualization of protein complexes
PredictProtein (US National Library of Medicine)
  • service for sequence analysis, structure and function prediction
PRINCESS (Beijing Institute of Radiation Medicine)
  • PRotein INteraction Confidence Evaluation System with multiple data Sources
ProSAT (EML Research gGmbH Heidelberg)
  • Protein Structure Annotation Tool
  • facilitate interactive visualization of non-structure-based functional annotations in protein 3D structures
ProSAT2 (EML Research gGmbH Heidelberg)
  • Protein Structure Annotation Server
  • server to select and group residue based annotations and explore them interactively on a 3D structure of a protein
Protopia (University of Malaga and CIBER de Enfermedades Raras, Department of Molecular Biology and Biochemistry, Faculty of Sciences, Instituto de Salud Carlos III)
  • biological tool that offers a way of searching proteins and their interactions in different Protein Interaction Web Databases
ProViz (Centre de Bioinformatique de Bordeaux)
  • protein-protein interaction graphs visualisation tool
Receptor Binding Domain Finder (University of Kaiserslautern)
  • tries to detect domains in a protein that might be involved in protein-protein interaction
SDA (EML Research gGmbH Heidelberg)
  • Simulation of Diffusional Association
  • permits Brownian dynamics simulations to be carried out and the rates of bimolecular diffusional association of 2 molecules, e.g. 2 proteins to be computed given the atomic structure of the bound complex of the 2 molecules
SHARP2 (University of Sussex)
  • predicts the location of protein interaction sites on the surface of the 3D structure of a protein
  • text-based approach
  • focus on the detection of interactions as they are reported in scientific and patent literature [PDF]
VANLO (Ernst-Moritz-Arndt-University)
  • interactive visual exploration of aligned biological networks
Vector PathBlazer™ (Informax Inc.)
  • ability to build, visualize and analyze biological pathways by using metabolic and protein-protein interaction data from multiple sources [PDF]
visANT (Boston University)
  • bio-network visualization and analysis tool
WebInterViewer (Inha University)
  • visualizes large-scale molecular interaction networks
webPIPSA (EML Research gGmbH)
  • Protein Interaction Property Similarity Analysis
  • web server for the comparison of protein interaction properties


Biological Data Mining in Protein Interaction Networks (Premier Reference Source)
See-Kiong Ng and Xiao-Li Lii
450 pp., Medical Information Science Reference, May 2009
ISBN: 978-1605663982 [Amazon]

Computational Approaches In Systems Biology: protein-protein interactions and its contribution in the Reconstruction of Metabolic Networks: A worm case study
Mahmood A. Mahdavi
124 pp., LAP Lambert Academic Publishing, August 2009
ISBN: 978-3838309682 [Amazon]

Computational Protein-Protein Interactions
Ruth Nussinov and Gideon Schreiber
343 pp., CRC Press, June 2009
ISBN: 978-1420070057 [Amazon]

Efficient Two-Stage Model for Predicting Protein-Protein Interactions: Machine Learning
Jingkai Yu
116 pp., VDM Verlag Dr. Müller, February 2009
ISBN: 978-3639118582 [Amazon]

Prediction of Protein Structures, Functions, and Interactions
Janusz Bujnicki
302 pp., Wiley; 1 edition, February 2009
ISBN: 978-0470517673 [Amazon]

Protein-protein Interactions and Networks: Identification, Computer Analysis, and Prediction (Computational Biology)
Anna Panchenko and Teresa Przytycka
212 pp., Springer, August 2008
ISBN: 978-1848001244 [Amazon]

Proteomics and Protein-Protein Interactions : Biology, Chemistry, Bioinformatics, and Drug Design (Protein Reviews)
Gabriel Waksman
324 pp., Springer, December 2005
ISBN: 978-0387245317 [Amazon]

Proteomics in Drug Research
Michael Hamacher, Katrin Marcus, Kai Stühler, Andre van Hall, Bettina Warscheid and Helmut E. Meyer
383 pp., Wiley-VCH, May 2006
ISBN: 978-3527312269 [Amazon]

Protein Structure Prediction (Methods in Molecular Biology)
Mohammed Zaki and Chris Bystroff
337 pp., Humana Press; 2nd edition, September 2007
ISBN: 978-1588297525 [Amazon]

Other information
Effiziente Algorithmen für das Protein-Docking-Problem. (by H.-P. Lenhof, Max-Planck-Institut für Informatik)
Molecular Docking Web (compiled by G.M. Morris, Scripps Research Institute)
Theoretical Protein-Protein Interaction Prediction. (by J. Jaffe et al., Harvard University)


   The Jena Protein-Protein Interaction Website