Comparative evaluation of eight docking tools for docking and virtual screening accuracy.
Kellenberger E, Rodrigo J, Muller P, Rognan D, Proteins, 2004 Nov 1 - link

A combinatorial approach to protein docking with flexible side chains.
Althaus E, Kohlbacher O, Lenhof HP, Muller P, J Comput Biol, 2002 - link