Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking.
Sivasubramanian A, Sircar A, Chaudhury S, Gray JJ, Proteins, 2009 Feb 1 - link

Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles.
Chaudhury S, Gray JJ, J Mol Biol, 2008 Sep 12 - link

The RosettaDock server for local protein-protein docking.
Lyskov S, Gray JJ, Nucleic Acids Res, 2008 Jul 1 - link

High-resolution protein-protein docking.
Gray JJ, Curr Opin Struct Biol, 2006 Apr - link

Structural model of the mAb 806-EGFR complex using computational docking followed by computational and experimental mutagenesis.
Sivasubramanian A, Chao G, Pressler HM, Wittrup KD, Gray JJ, Structure, 2006 Mar - 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