PTools: an opensource molecular docking library.
Saladin A, Fiorucci S, Poulain P, Prevost C, Zacharias M, BMC Struct Biol, 2009 May 1 - link

Accounting for loop flexibility during protein-protein docking.
Bastard K, Prevost C, Zacharias M, Proteins, 2006 Mar 1 - link

Docking macromolecules with flexible segments.
Bastard K, Thureau A, Lavery R, Prevost C, J Comput Chem, 2003 Nov 30 - link