Wikiomics:Docking toolbox
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Following programs are used for docking small molecules into protein pockets/active sites: | Following programs are used for docking small molecules into protein pockets/active sites: | ||
| - | == | + | ==Commercial== |
| - | * | + | * [http://www.biosolveit.de/FlexX/ FlexX ] (both stand alone and Sybyl/MOE module) Sybyl docking tutorial: [http://www.cmbi.ru.nl/edu/bioinf4/thu-Prac/screening/screenings.shtml] $$$ |
| - | * | + | * [http://www.ccdc.cam.ac.uk/products/life_sciences/gold/ GOLD ] $$$ |
| - | * | + | * [http://www.molsoft.com/docking.html ICM] (docking)$$$ |
| - | * | + | * [http://www.schrodinger.com/ProductDescription.php?mID=6&sID=6 GLIDE] $$$ |
==Free/Semi Free??== | ==Free/Semi Free??== | ||
!! needs verification as of Nov 2006!! | !! needs verification as of Nov 2006!! | ||
| - | * | + | * [http://autodock.scripps.edu/ AutoDock] |
| - | * | + | * [http://dock.compbio.ucsf.edu/ DOCK] from UCSF . Rigid and Flexible Ligand Docking. |
| - | * | + | |
| + | * [http://gemdock.life.nctu.edu.tw/dock/ GEMDOCK] | ||
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| + | =Ligands databases= | ||
| + | * [http://ligand.info/ Ligand.Info] Small-Molecule Meta-Database | ||
| + | * [http://zinc.docking.org/ ZINC] a free database of commercially-available compounds for virtual screening | ||
| - | ==Reviews== | + | ==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. | * 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. | ||
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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] | ||
== Credits == | == Credits == | ||
Revision as of 08:40, 18 January 2008
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!!
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]
Credits
- Darek Kedra wrote this tutorial
