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Following programs are used for docking small molecules into protein pockets/active sites:
- FlexX (both stand alone and Sybyl/MOE module) Sybyl docking tutorial: 
- ICM (docking)
- Materials Studio
!! needs verification as of Nov 2006!!
- 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
- 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 
- 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]
- 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.
- Darek Kedra wrote this tutorial