Following programs are used for docking small molecules into protein pockets/active sites:
- FlexX (both stand alone and Sybyl/MOE module) Sybyl docking tutorial:  $$$
- GOLD $$$
- ICM (docking)$$$
- GLIDE $$$
!! needs verification as of Nov 2006!!
- Ligand.Info Small-Molecule Meta-Database
- ZINC a free database of commercially-available compounds for virtual screening
- 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 
- Darek Kedra wrote this tutorial