Wikiomics:Docking toolbox

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:
 * GOLD
 * ICM (docking)
 * GLIDE
 * Materials Studio
 * ArgusLab

Free/Semi Free??
!! needs verification as of Nov 2006!!


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


 * GEMDOCK
 * SwissDock

=Ligands databases=
 * Ligand.Info Small-Molecule Meta-Database
 * ZINC a free database of commercially-available compounds for virtual screening
 * LPDB. Curated target and ligand structures
 * S3DBDatabase of manually 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


 * very good review by Aatu Kaapro Janne Ojanen from 2002:
 * 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.
 * HEX

Credits

 * Darek Kedra wrote this tutorial