Comparison of some representative density functional theory and wave function theory methods for the studies of amino acids. - Wenbo Yu 002; Lei Liang; Zijing Lin; Sanliang Ling; Maciej Haranczyk; Maciej Gutowski (J. Comput. Chem., 2009)

Extensive conformational searches of 13 representative dipeptides and an efficient method for dipeptide structure determinations based on amino acid conformers. - Wenbo Yu 002; Xuee Xu; Hongbao Li; Rui Pang; Kun Fang; Zijing Lin (J. Comput. Chem., 2009)

Reproducing Crystal Binding Modes of Ligand Functional Groups Using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations. - E. Prabhu Raman; Wenbo Yu 002; Olgun Guvench; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2011)

Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations. - Wenbo Yu 002; Xibing He; Kenno Vanommeslaeghe; Alexander D. MacKerell Jr. (J. Comput. Chem., 2012)

Inclusion of Multiple Fragment Types in the Site Identification by Ligand Competitive Saturation (SILCS) Approach. - E. Prabhu Raman; Wenbo Yu 002; Sirish Kaushik Lakkaraju; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2013)

Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling. - Wenbo Yu 002; Sirish Kaushik Lakkaraju; E. Prabhu Raman; Alexander D. MacKerell Jr. (J. Comput. Aided Mol. Des., 2014)

Mapping Functional Group Free Energy Patterns at Protein Occluded Sites: Nuclear Receptors and G-Protein Coupled Receptors. - Sirish Kaushik Lakkaraju; Wenbo Yu 002; E. Prabhu Raman; Alena V. Hershfeld; Lei Fang; Deepak Deshpande; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2015)

Pharmacophore Modeling Using Site-Identification by Ligand Competitive Saturation (SILCS) with Multiple Probe Molecules. - Wenbo Yu 002; Sirish Kaushik Lakkaraju; E. Prabhu Raman; Lei Fang; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2015)

Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization. - Vincent D. Ustach; Sirish Kaushik Lakkaraju; Sunhwan Jo; Wenbo Yu 002; Wenjuan Jiang; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2019)

Detection of Putative Ligand Dissociation Pathways in Proteins Using Site-Identification by Ligand Competitive Saturation. - Wenbo Yu 002; David J. Weber; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2025)