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!!
- 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: 
- Darek Kedra wrote this tutorial