Wikiomics:Docking toolbox: Difference between revisions
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Darek Kedra (talk | contribs) m (protein 2 protein docking) |
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* very good review by Aatu Kaapro Janne Ojanen from 2002: [http://www.lce.hut.fi/teaching/S-114.500/2002/Protdock.pdf] | * very good review by Aatu Kaapro Janne Ojanen from 2002: [http://www.lce.hut.fi/teaching/S-114.500/2002/Protdock.pdf] | ||
* UCSF docking [http://wiki.compbio.ucsf.edu/wiki/index.php/Main_Page wiki] | * UCSF docking [http://wiki.compbio.ucsf.edu/wiki/index.php/Main_Page wiki] | ||
=Protein-protein docking= | |||
* [http://zdock.bu.edu/ 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 | |||
== Credits == | == Credits == | ||
Revision as of 16:38, 11 August 2008
Following programs are used for docking small molecules into protein pockets/active sites:
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!!
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]
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
Credits
- Darek Kedra wrote this tutorial
