Difference between revisions of "Wikiomics:Docking toolbox"

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(Ligands databases)
(Free/Semi Free??)
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* [http://gemdock.life.nctu.edu.tw/dock/ GEMDOCK]
* [http://gemdock.life.nctu.edu.tw/dock/ GEMDOCK]
* [http://swissdock.vital-it.ch/ SwissDock]
=Ligands databases=
=Ligands databases=

Revision as of 13:48, 19 October 2010

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


Free/Semi Free??

!! needs verification as of Nov 2006!!

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

Ligands databases


  • 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.