Protein-protein docking dealing with the unknown.
Moreira IS, Fernandes PA, Ramos MJ, J Comput Chem, 2009 May 21 - link

MADAMM: a multistaged docking with an automated molecular modeling protocol.
Cerqueira NM, Bras NF, Fernandes PA, Ramos MJ, Proteins, 2009 Jan - link

Protein-ligand docking: current status and future challenges.
Sousa SF, Fernandes PA, Ramos MJ, Proteins, 2006 Oct 1 - link