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)

Exact multiplicity and stability of solutions of second-order Neumann boundary value problem. - Hui Xing; Hongbin Chen 003; Xibing He (Appl. Math. Comput., 2014)

Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates. - Meagan C. Small; Asaminew H. Aytenfisu; Fang-Yu Lin; Xibing He; Alexander D. MacKerell Jr. (J. Comput. Aided Mol. Des., 2017)

Significantly different effects of tetrahydroberberrubine enantiomers on dopamine D1/D2 receptors revealed by experimental study and integrated in silico simulation. - Haixia Ge; Yuemin Bian; Xibing He; Xiang-Qun Xie; Junmei Wang (J. Comput. Aided Mol. Des., 2019)

Calculate protein-ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3. - Xibing He; Viet Hoang Man; Beihong Ji; Xiang-Qun Xie; Junmei Wang (J. Comput. Aided Mol. Des., 2019)

How Well Does the Extended Linear Interaction Energy Method Perform in Accurate Binding Free Energy Calculations? - Dongxiao Hao; Xibing He; Beihong Ji; Shengli Zhang; Junmei Wang (J. Chem. Inf. Model., 2020)

Machine learning on ligand-residue interaction profiles to significantly improve binding affinity prediction. - Beihong Ji; Xibing He; Jingchen Zhai; Yuzhao Zhang; Viet Hoang Man; Junmei Wang (Briefings Bioinform., 2021)

In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. - Yuzhao Zhang; Xibing He; Jingchen Zhai; Beihong Ji; Viet Hoang Man; Junmei Wang (Briefings Bioinform., 2021)

Incorporating structural similarity into a scoring function to enhance the prediction of binding affinities. - Beihong Ji; Xibing He; Yuzhao Zhang; Jingchen Zhai; Viet Hoang Man; Shuhan Liu; Junmei Wang (J. Cheminformatics, 2021)

Stable Cavitation Interferes with Aβ16-22 Oligomerization. - Viet Hoang Man; Xibing He; Junmei Wang (J. Chem. Inf. Model., 2022)

Development and test of highly accurate endpoint free energy methods. 1: Evaluation of ABCG2 charge model on solvation free energy prediction and optimization of atom radii suitable for more accurate solvation free energy prediction by the PBSA method. - Yuchen Sun; Xibing He; Tingjun Hou; Lianjin Cai; Viet Hoang Man; Junmei Wang (J. Comput. Chem., 2023)

Development and test of highly accurate endpoint free energy methods. 2: Prediction of logarithm of n-octanol-water partition coefficient (logP) for druglike molecules using MM-PBSA method. - Yuchen Sun; Tingjun Hou; Xibing He; Viet Hoang Man; Junmei Wang (J. Comput. Chem., 2023)

Phosphorylation at Ser289 Enhances the Oligomerization of Tau Repeat R2. - Viet Hoang Man; Xibing He; Fengyang Han; Lianjin Cai; Luxuan Wang; Taoyu Niu; Jingchen Zhai; Beihong Ji; Jie Gao; Junmei Wang (J. Chem. Inf. Model., 2023)

Unpolarized laser method for infrared spectrum calculation of amide I C=O bonds in proteins using molecular dynamics simulation. - Viet Hoang Man; Xibing He; Phuong H. Nguyen; Celeste Sagui; Christopher Roland; Xiang-Qun Xie; Junmei Wang (Comput. Biol. Medicine, 2023)

Distribution of Bound Conformations in Conformational Ensembles for X-ray Ligands Predicted by the ANI-2X Machine Learning Potential. - Fengyang Han; Dongxiao Hao; Xibing He; Luxuan Wang; Taoyu Niu; Junmei Wang (J. Chem. Inf. Model., 2023)

Effects of All-Atom and Coarse-Grained Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of a Tau K18 Monomer. - Xibing He; Viet Hoang Man; Jie Gao; Junmei Wang (J. Chem. Inf. Model., 2024)