Wenbo Yu

11 papers Journal 11
YearRankTypeTitle / Venue / Authors
2026 J jnl
Computational Modeling of PROTAC Ternary Complexes as Ensembles Using SILCS-xTAC.
J. Chem. Inf. Model.
Erik B. Nordquist, Mingtian Zhao, Wenbo Yu, Alexander D. MacKerell Jr.
2025 J jnl
Detection of Putative Ligand Dissociation Pathways in Proteins Using Site-Identification by Ligand Competitive Saturation.
J. Chem. Inf. Model.
Wenbo Yu, David J. Weber, Alexander D. MacKerell Jr.
2019 J jnl
Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization.
J. Chem. Inf. Model.
Vincent D. Ustach, Sirish Kaushik Lakkaraju, Sunhwan Jo, Wenbo Yu, Wenjuan Jiang, Alexander D. MacKerell Jr.
2015 J jnl
Mapping Functional Group Free Energy Patterns at Protein Occluded Sites: Nuclear Receptors and G-Protein Coupled Receptors.
J. Chem. Inf. Model.
Sirish Kaushik Lakkaraju, Wenbo Yu, E. Prabhu Raman, Alena V. Hershfeld, Lei Fang, Deepak Deshpande, Alexander D. MacKerell Jr.
2015 J jnl
Pharmacophore Modeling Using Site-Identification by Ligand Competitive Saturation (SILCS) with Multiple Probe Molecules.
J. Chem. Inf. Model.
Wenbo Yu, Sirish Kaushik Lakkaraju, E. Prabhu Raman, Lei Fang, Alexander D. MacKerell Jr.
2014 J jnl
Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling.
J. Comput. Aided Mol. Des.
Wenbo Yu, Sirish Kaushik Lakkaraju, E. Prabhu Raman, Alexander D. MacKerell Jr.
2013 J jnl
Inclusion of Multiple Fragment Types in the Site Identification by Ligand Competitive Saturation (SILCS) Approach.
J. Chem. Inf. Model.
E. Prabhu Raman, Wenbo Yu, Sirish Kaushik Lakkaraju, Alexander D. MacKerell Jr.
2012 J jnl
Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations.
J. Comput. Chem.
Wenbo Yu, Xibing He, Kenno Vanommeslaeghe, Alexander D. MacKerell Jr.
2011 J jnl
Reproducing Crystal Binding Modes of Ligand Functional Groups Using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations.
J. Chem. Inf. Model.
E. Prabhu Raman, Wenbo Yu, Olgun Guvench, Alexander D. MacKerell Jr.
2009 J jnl
Comparison of some representative density functional theory and wave function theory methods for the studies of amino acids.
J. Comput. Chem.
Wenbo Yu, Lei Liang, Zijing Lin, Sanliang Ling, Maciej Haranczyk, Maciej Gutowski
2009 J jnl
Extensive conformational searches of 13 representative dipeptides and an efficient method for dipeptide structure determinations based on amino acid conformers.
J. Comput. Chem.
Wenbo Yu, Xuee Xu, Hongbao Li, Rui Pang, Kun Fang, Zijing Lin