Simultaneous prediction of protein folding and docking at high resolution.
Das R, Andre I, Shen Y, Wu Y, Lemak A, Bansal S, Arrowsmith CH, Szyperski T, Baker D, Proc Natl Acad Sci U S A, 2009 Nov 10 - link

Blind docking of pharmaceutically relevant compounds using RosettaLigand.
Davis IW, Raha K, Head MS, Baker D, Protein Sci, 2009 Sep - link

RosettaLigand docking with full ligand and receptor flexibility.
Davis IW, Baker D, J Mol Biol, 2009 Jan 16 - link

Protein-protein docking with backbone flexibility.
Wang C, Bradley P, Baker D, J Mol Biol, 2007 Oct 19 - link

ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility.
Meiler J, Baker D, Proteins, 2006 Nov 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