Wikiomics:Docking toolbox

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(Protein-protein docking)
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** ZRANK
** ZRANK
** RDOCK
** RDOCK
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*[http://www.loria.fr/~ritchied/hex/ HEX] Hex is an interactive protein docking and molecular superposition program.It takes protein and DNA PDB file format and also read small-molecule SDF files.
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** [http://www.loria.fr/~ritchied/hex/licence.html HEX]

Revision as of 07:21, 18 January 2010



Following programs are used for docking small molecules into protein pockets/active sites:

Contents

Commercial

  • FlexX (both stand alone and Sybyl/MOE module) Sybyl docking tutorial: [1] $$$
  • GOLD $$$
  • ICM (docking)$$$
  • GLIDE $$$

Free/Semi Free??

!! needs verification as of Nov 2006!!

  • AutoDock
  • DOCK from UCSF . Rigid and Flexible Ligand Docking.

Ligands databases

  • Ligand.Info Small-Molecule Meta-Database
  • ZINC a free database of commercially-available compounds for virtual screening

Reviews/Info

  • Sperandio O, Miteva MA, Delfaud F, Villoutreix Receptor-based computational screening of compound databases: the main docking-scoring engines.Curr Protein Pept Sci. 2006 Oct;7(5):369-93.
  • Muegge, M Rarey - mall molecule docking and scoring Reviews in Computational Chemistry, Dec 2001 [2]
  • very good review by Aatu Kaapro Janne Ojanen from 2002: [3]
  • UCSF docking wiki

Protein-protein docking

  • ZDOCK rigid docking, "Fast Fourier Transform based protein docking program. It takes two PDB files and outputs the predicted structure of their complex" See also: http://wiki.bioinformatics.org/ZDOCK @bioinformatics.org]
    • M-ZDOCK
    • ZRANK
    • RDOCK
  • HEX Hex is an interactive protein docking and molecular superposition program.It takes protein and DNA PDB file format and also read small-molecule SDF files.


Credits

Template:Credits

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