Wikiomics:Docking toolbox: Difference between revisions
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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:
Commercial
- FlexX (both stand alone and Sybyl/MOE module) Sybyl docking tutorial: [1] $$$
- GOLD $$$
- ICM (docking)$$$
- GLIDE $$$
- Materials Studio
- ArgusLab$$$
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
- Ligand-Protein Database. Curated target and ligand structures
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
- 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
- Darek Kedra wrote this tutorial
