Jinjiang's WebWatcher on Biology (5) - protein-protein docking tools

Web based tools
 • PREPPI: A web service to predict protein-protein interactions by combining structural and non-structural information.
 • PredUs: A tool to predict protein-protein interface based on interface conservation among structurally similar protein neighbors.
 • PUDGE: This protein structure prediction server provides a convenient means of integrating tools that may be used at different stages of the structural prediction process.
 • Mark-Us: A Function Annotation Server for Protein Structures.
 • Target Explorer: A web based tool for automatic identification of new target genes for transcription factors in the Drosophila genome.
 • EDGI: (Enhancer Detection using only Genomic Information) discovers transcriptional regulatory regions in Drosophila by a non-alignment method for phylogenetic footprinting.
 • Model Quality Assessment: Global and Local Quality Assessment of Protein Models.
 • STING Millennium: A web based suite of programs for comprehensive and simultaneous analysis of structure and sequence: nature and volume of atomic contacts of both intra- and inter- chain types, analysis of the quality of structure, residue conservation and its relationship with intra-chain contacts, functional parameters are also deciphered.
 • SCREEN: A web server tool for identifying protein cavities and computing cavity attributes that can be applied for classification and analysis.
 • RoettaDock server at http://rosettadock.graylab.jhu.edu/
 • HADDOCK at http://haddock.science.uu.nl
 • Cluspro 2.0 (with antibody mode):http://cluspro.bu.edu/login.php
 •  HEX 6.3: http://hex.loria.fr
 • GRAMMX (Vakser Tool) online or ZDOCK
 • prediction tools for interfaces - CPORT;  http://haddock.science.uu.nl/services/CPORT
 • Vina http://vina.scripps.edu/
 •  PS2 http://ps2.life.nctu.edu.tw/

 • STRAP java,  for comparing multiple PDB and visualisation 3D structure
--  http://www.charite.de/bioinf/strap/Scripting.html
 • BALLView -- http://www.ball-project.org/Ballview
 • Structural Analysis and Verification Server: http://nihserver.mbi.ucla.edu/SAVES/