DARS (Decoys As the Reference State) potentials for protein-protein docking.
Chuang GY, Kozakov D, Brenke R, Comeau SR, Vajda S, Biophys J, 2008 Nov 1 - link

Docking with PIPER and refinement with SDU in rounds 6-11 of CAPRI.
Shen Y, Brenke R, Kozakov D, Comeau SR, Beglov D, Vajda S, Proteins, 2007 Dec 1 - link

PIPER: an FFT-based protein docking program with pairwise potentials.
Kozakov D, Brenke R, Comeau SR, Vajda S, Proteins, 2006 Nov 1 - link

Performance of the first protein docking server ClusPro in CAPRI rounds 3-5.
Comeau SR, Vajda S, Camacho CJ, Proteins, 2005 Aug 1 - link

ClusPro: a fully automated algorithm for protein-protein docking.
Comeau SR, Gatchell DW, Vajda S, Camacho CJ, Nucleic Acids Res, 2004 Jul 1 - link

ClusPro: an automated docking and discrimination method for the prediction of protein complexes.
Comeau SR, Gatchell DW, Vajda S, Camacho CJ, Bioinformatics, 2004 Jan 1 - link