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

Protein docking by the underestimation of free energy funnels in the space of encounter complexes.
Shen Y, Paschalidis ICh, Vakili P, Vajda S, PLoS Comput Biol, 2008 Oct - link

Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels.
Paschalidis ICh, Shen Y, Vakili P, Vajda S, Conf Proc IEEE Eng Med Biol Soc, 2006 - 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

SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking.
Paschalidis IC, Shen Y, Vakili P, Vajda S, IEEE Trans Automat Contr, 2007 Apr 1 - link

Redundant roles for Met docking site tyrosines and the Gab1 pleckstrin homology domain in InlB-mediated entry of Listeria monocytogenes.
Basar T, Shen Y, Ireton K, Infect Immun, 2005 Apr - link