Question

Which is the best free online tool available for protein-protein docking ?

Am having problems in getting the best interacting postions..... thank u frnds for the help. i have already tried hex. it shows the docking but not the exact region of interaction.is there a way to do it?
i will now try other tools. thanxx again.
Jan 28, 2012

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  • Carlos Del Carpio · Kyoto Institute of Technology
    I don't think such a tool exists... There are programs that can give you candidates (servers, just make a google search), but not the exact solution... This problem as well as the protein 3D structure prediction problem are still matter of huge investigation...
    Jan 29, 2012
  • Carlos Del Carpio · Kyoto Institute of Technology
    MIAX is a system that I have been developing for years, so if you have your proteins, you can give me your PDB codes, and see what candidates I can predict for you... though as I told you before, there are not programs that will give you the close-to-native solution one may require...
    Jan 29, 2012
  • Constantinos Vorgias · National and Kapodistrian University of Athens
    Ask in Holland, Utrecht University, NMR Department. Panagiotis Kastritsis will certainly help you.
    Jan 29, 2012
  • Rosangela Hickson · Faculdade Infórium de Tecnologia
    I work with docking protein-protein and ligand-protein in Brasil.
    We work together with IBM to find new drugs for Schistosoma Mansoni, using VINA.
    There are many tools.
    Vina, Chimera, Autodock tools, PyRx, PMV, Vision and so one.
    Jan 29, 2012
  • Yi Xiong · Purdue University
    such as Z-dock
    Jan 29, 2012
  • Ejaz Ahmad · Aligarh Muslim University
    Hex Protein Docking Server

    http://hexserver.loria.fr/

    Reference:
    Macindoe G, Mavridis L, Venkatraman V, Devignes MD, Ritchie DW. HexServer: an FFT-based protein docking server powered by graphics processors.Nucleic Acids Res. 2010; 38 (Web Server issue): W445-449.
    Jan 29, 2012
  • Jose Gavira · Spanish National Research Council
    http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
    "PDBePISA is an interactive tool for the exploration of macromolecular (protein, DNA/RNA and ligand) interfaces, prediction of probable quaternary structures (assemblies), database searches of structurally similar interfaces and assemblies, as well as searches on various assembly and PDB entry parameters."
    Jan 29, 2012
  • Renton Innes ·
    Robetta ( Rosetta ) Fold.it Baker Labs UW protein docking software add on. Protein Folding Rules !
    Jan 29, 2012
  • Rajashri Bhairamadgi · Academisch Medisch Centrum Universiteit van Amsterdam
    http://bioinformatictools.blogspot.nl/2011/12/protein-protein-docking-servers.html

    this link will provide you a list of Protein-Protein docking tools. Try the servers from the list.
    Jul 10, 2012

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