Novel PPAR-gamma agonists identified from a natural product library: a virtual screening, induced-fit docking and biological assay study.
Salam NK, Huang TH, Kota BP, Kim MS, Li Y, Hibbs DE, Chem Biol Drug Des, 2008 Jan - link

Progressive docking: a hybrid QSAR/docking approach for accelerating in silico high throughput screening.
Cherkasov A, Ban F, Li Y, Fallahi M, Hammond GL, J Med Chem, 2006 Dec 14 - link

Predicting substrates by docking high-energy intermediates to enzyme structures.
Hermann JC, Ghanem E, Li Y, Raushel FM, Irwin JJ, Shoichet BK, J Am Chem Soc, 2006 Dec 13 - link

Anti-SARS drug screening by molecular docking.
Wei DQ, Zhang R, Du QS, Gao WN, Li Y, Gao H, Wang SQ, Zhang X, Li AX, Sirois S, Chou KC, Amino Acids, 2006 Jul - link

'Inductive' charges on atoms in proteins: comparative docking with the extended steroid benchmark set and discovery of a novel SHBG ligand.
Cherkasov A, Shi Z, Li Y, Jones SJ, Fallahi M, Hammond GL, J Chem Inf Model, 2005 Nov-Dec - link

Temperature differentially affects encounter and docking thermodynamics of antibody--antigen association.
Lipschultz CA, Yee A, Mohan S, Li Y, Smith-Gill SJ, J Mol Recognit, 2002 Jan-Feb - link

Thermodynamic and activation parameters for binding of a pyrene-labeled substrate by the Tetrahymena ribozyme: docking is not diffusion-controlled and is driven by a favorable entropy change.
Li Y, Bevilacqua PC, Mathews D, Turner DH, Biochemistry, 1995 Nov 7 - link

Fluorescence-detected stopped flow with a pyrene labeled substrate reveals that guanosine facilitates docking of the 5' cleavage site into a high free energy binding mode in the Tetrahymena ribozyme.
Bevilacqua PC, Li Y, Turner DH, Biochemistry, 1994 Sep 20 - link