Discrimination of near-native structures in protein-protein docking by testing the stability of local minima.
Kozakov D, Schueler-Furman O, Vajda S, Proteins, 2008 Aug 15 - link

Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility.
Schueler-Furman O, Wang C, Baker D, Proteins, 2005 Aug 1 - link

Improved side-chain modeling for protein-protein docking.
Wang C, Schueler-Furman O, Baker D, Protein Sci, 2005 May - link

Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.
Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D, J Mol Biol, 2003 Aug 1 - link

Protein-protein docking predictions for the CAPRI experiment.
Gray JJ, Moughon SE, Kortemme T, Schueler-Furman O, Misura KM, Morozov AV, Baker D, Proteins, 2003 Jul 1 - link