![]() |
|
Software | |
![]() |
|
Books | Other information |
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. | [PDF] |
[PubMed] |
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. | [PDF] |
[PubMed] |
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. | [PDF] |
[PubMed] |
Vajda, S.; Camacho, C.J.; Trends Biotechnol. 2004, 22(3), 110-116. Protein-protein docking: is the glass half-full or half-empty? | [PDF] |
[PubMed] |
Xenarios, I.; Eisenberg, D.; Curr. Opin. Biotechnol. 2001, 12(4), 334-339. Protein interaction databases. | [PubMed] |
Prediction contest CAPRI |
CAPRI - Critical Assessment of PRedicted Interactions | ||
Meeting report 2001: Modeling of protein interactions in genomes | [HTML] |
|
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. | [PDF] |
[PubMed] |
Janin, J.; Protein Sci. 2005, 14(2), 278-283. Assessing predictions of protein-protein interaction: the CAPRI experiment. | [PDF] |
[PubMed] |
Janin, J.; Proteins 2007, 69(4), 699-703. The targets of CAPRI rounds 6-12. | [PubMed] |
|
Janin, J.; Wodak, S.; Structure 2007, 15(7), 755-759. The third CAPRI assessment meeting Toronto, Canada, April 20-21, 2007. | [PubMed] |
|
Lensink, M.F.; Méndez, R.; Wodak, S.J.; Proteins 2007, 69(4), 704-718. Docking and scoring protein complexes: CAPRI 3rd eEdition. | [PubMed] |
Software |
Protein-protein (peptide) docking
3D-Dock Suite (BioMolecular Modeling, Cancer Research UK) |
|
3D-Garden (Imperial College London) |
|
Bielefeld Protein Docking (Bielefeld University) |
|
BiGGER (BioTecnol, S.A.) |
|
ClusPro (Boston University) |
|
DOT (San Diego Supercomputer Center) |
|
ESCHER NG (Milan University) |
|
FireDock (Tel Aviv University & Center for Cancer Research Nanobiology Program) |
|
HADDOCK (Utrecht University Netherlands) |
|
HEX (University of Aberdeen) |
|
RosettaDock Server (Johns Hopkins University) |
|
Software |
Protein-ligand docking
Affinity (Accelrys Inc.) |
AutoDock (The Scripps Research Institute) |
CombiBUILD (Sandia National Labs) |
|
DockVision (University of Alberta) |
eHiTS (SimBioSys Inc.) |
|
FRED (OpenEye) |
|
FlexiDock (Tripos) |
FlexX (BioSolveIT GmbH) |
GLIDE (Schrödinger GmbH) |
GOLD (CCDC) |
HINT (Virginia Commonwealth University) |
|
LIGPLOT (University College of London) |
|
POCASA (Graduate School of Life Science) |
|
Pocket- Finder (University of Leeds) |
|
Q-SiteFinder (University of Leeds) |
|
QUANTUM (Quantum Pharmaceuticals) |
|
SITUS (Scripps Research Institute) |
|
VEGA (Milan University) |
|
Software |
Protein-protein and protein ligand docking
DOCK (UCSF Molecular Design Institute) |
GRAMM (SUNY) |
|
ICM-Docking (MolSoft LLC) |
PatchDock (Tel Aviv University) |
|
Software |
Related programs for analysis and visualization
aiSee (AbsInt Angewandte Informatik GmbH) |
|
APID (Cancer Research Center) |
|
APID2NET (Cancer Research Center) |
|
AVIS (Mount Sinai School of Medicine) |
|
BioJAKE (BIC Singapore) |
|
BIOSMILE (National Tsing-Hua University & Yuan Ze University) |
|
Bioverse (University of Washington) |
|
COCOMAPS (University of Salerno & University of Napoli 'Parthenope' ) |
|
Cytoscape (Institute for Systems Biology & Whitehead Institute for Biomedical Research) |
|
dockYard (Indian Institute of Science) |
|
Drugscore-PPI (Heinrich-Heine-University) |
|
Dynamic Signaling Maps™ (Hippron Physiomics) |
|
EXpanda (Keio University) |
|
GenoMax™ (Informax) |
|
GRAMM-X (University of Kansas) |
|
Graphviz (AT&T Research) |
|
HARMONY (The Scripps Research Institute) |
|
HotDock (University Paderborn) |
|
I2I-SiteEngine (Tel Aviv University) |
|
iMolTalk (Swiss Institute of Bioinformatics) |
|
Integrator (University of Washington School of Medicine) |
|
InteroPorc (IBITECS) |
|
InterProSurf (University of Texas Medical Branch) |
|
InterViewer (Inha University, WI Lab) |
|
iPfam (Sanger Institute) |
|
iVici (Universite de Montreal, Canada) |
|
Java 3D – MPI (University Georgia) |
|
jSquid (Stockholm University) |
|
KFC Server (University of Wisconsin-Madison) |
|
MaGnET (University of Edinburgh) |
|
metaPocket (EML Research gGmbH) |
|
MidasPlus (UCSF, Computer Graphics Lab) |
|
Moksiskaan (University of Helsinki) |
|
MolSurfer (EML Research gGmbH Heidelberg) |
NAViGaTOR (University of Toronto) |
|
Osprey (Samuel Lunenfeld Research Institute) |
|
PathDB™ (NCGR) |
|
PathwayAssist™ (Ariadne Genomics) |
|
PIANA (Structural Bioinformatics Group (GRIB-IMIM), Universitat Pompeu Fabra) |
|
PIE (Seoul National University & National Institute of Standards and Technology) |
|
PIMRider® (Hybrigenics) |
|
PIPSA (EML Research gGmbH Heidelberg) |
|
PI-SCOUT™ (LION biosience) |
|
Plasmodium falciparum Protein-Protein Interaction Network (Princeton University) |
|
PolySearch (University of Alberta) |
|
POLYVIEW-3D (University of Cincinnati) |
|
PredictProtein (US National Library of Medicine) |
|
PRINCESS (Beijing Institute of Radiation Medicine) |
|
ProSAT (EML Research gGmbH Heidelberg) |
|
ProSAT2 (EML Research gGmbH Heidelberg) |
|
Protopia (University of Malaga and CIBER de Enfermedades Raras, Department of Molecular Biology and Biochemistry, Faculty of Sciences, Instituto de Salud Carlos III) |
|
ProViz (Centre de Bioinformatique de Bordeaux) |
|
Receptor Binding Domain Finder (University of Kaiserslautern) |
|
SDA (EML Research gGmbH Heidelberg) |
|
SHARP2 (University of Sussex) |
|
TEMIS (TEMIS S.A.) |
|
VANLO (Ernst-Moritz-Arndt-University) |
|
Vector PathBlazer™ (Informax Inc.) |
|
visANT (Boston University) |
|
WebInterViewer (Inha University) |
|
webPIPSA (EML Research gGmbH) |
|
Books |
![]() |
|
![]() |
|
![]() |
|
![]() |
|
![]() |
|
![]() |
|
![]() |
|
![]() |
|
![]() |
|
Other information |
Effiziente Algorithmen für das Protein-Docking-Problem. (by H.-P. Lenhof, Max-Planck-Institut für Informatik) | [HTML] |
Molecular Docking Web (compiled by G.M. Morris, Scripps Research Institute) | |
Theoretical Protein-Protein Interaction Prediction. (by J. Jaffe et al., Harvard University) | [HTML] |