An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles.
Xu B, Yang Y, Liang H, Zhou Y, Proteins, 2009 Aug 15 - link

Refining near-native protein-protein docking decoys by local resampling and energy minimization.
Liang S, Wang G, Zhou Y, Proteins, 2009 Aug 1 - link

Consensus scoring for enriching near-native structures from protein-protein docking decoys.
Liang S, Meroueh SO, Wang G, Qiu C, Zhou Y, Proteins, 2009 May 1 - link

A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys.
Liang S, Liu S, Zhang C, Zhou Y, Proteins, 2007 Nov 1 - link

3D-QSAR and molecular docking studies on benzothiazole derivatives as Candida albicans N-myristoyltransferase inhibitors.
Sheng C, Zhu J, Zhang W, Zhang M, Ji H, Song Y, Xu H, Yao J, Miao Z, Zhou Y, Zhu J, Lu J, Eur J Med Chem, 2007 Apr - link

Structure-based optimization of azole antifungal agents by CoMFA, CoMSIA, and molecular docking.
Sheng C, Zhang W, Ji H, Zhang M, Song Y, Xu H, Zhu J, Miao Z, Jiang Q, Yao J, Zhou Y, Zhu J, Lu J, J Med Chem, 2006 Apr 20 - link

Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function.
Zhang C, Liu S, Zhou Y, Proteins, 2005 Aug 1 - link