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Following programs are used for docking small molecules into protein pockets/active sites:

Commercial

!! needs verification as of Nov 2006!!

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]

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

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 * [http://ligand.info/ Ligand.Info] Small-Molecule Meta-Database
 * [http://zinc.docking.org/ ZINC] a free database of commercially-available compounds for virtual screening
-* [http://lpdb.chem.lsa.umich.edu/ Ligand-Protein Database.] Curated target and ligand structures
+* [http://lpdb.chem.lsa.umich.edu/ LPDB.] Curated target and ligand structures
-* [http://swissdock.vital-it.ch/s3db/index.php Ligand-Protein Database.]Database of manually curated target and ligand structures
+* [http://swissdock.vital-it.ch/s3db/index.php S3DB]Database of manually curated target and ligand structures
 ==Reviews/Info==