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: [1]
• 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 [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.
  • HEX

Credits

• Darek Kedra wrote this tutorial