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Journal Articles
- 2023
[j15]Viet Hoang Man
, Xibing He, Phuong H. Nguyen, Celeste Sagui, Christopher Roland, Xiang-Qun Xie, Junmei Wang:
Unpolarized laser method for infrared spectrum calculation of amide I C=O bonds in proteins using molecular dynamics simulation. Comput. Biol. Medicine 159: 106902 (2023)- [j14]Yuchen Sun, Tingjun Hou, Xibing He, Viet Hoang Man, Junmei Wang:
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. J. Comput. Chem. 44(13): 1300-1311 (2023) - [j13]Yuchen Sun, Xibing He, Tingjun Hou, Lianjin Cai, Viet Hoang Man, Junmei Wang:
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. J. Comput. Chem. 44(14): 1334-1346 (2023) - [j12]Viet Hoang Man, Xibing He, Fengyang Han, Lianjin Cai, Luxuan Wang, Taoyu Niu, Jingchen Zhai, Beihong Ji, Jie Gao, Junmei Wang:
Phosphorylation at Ser289 Enhances the Oligomerization of Tau Repeat R2. J. Chem. Inf. Model. 63(4): 1351-1361 (2023) - [j11]Fengyang Han, Dongxiao Hao, Xibing He, Luxuan Wang, Taoyu Niu, Junmei Wang:
Distribution of Bound Conformations in Conformational Ensembles for X-ray Ligands Predicted by the ANI-2X Machine Learning Potential. J. Chem. Inf. Model. 63(21): 6608-6618 (2023) - 2022
- [j10]Viet Hoang Man, Xibing He, Junmei Wang:
Stable Cavitation Interferes with Aβ16-22 Oligomerization. J. Chem. Inf. Model. 62(16): 3885-3895 (2022) - 2021
- [j9]Beihong Ji, Xibing He, Jingchen Zhai, Yuzhao Zhang, Viet Hoang Man, Junmei Wang:
Machine learning on ligand-residue interaction profiles to significantly improve binding affinity prediction. Briefings Bioinform. 22(5) (2021) - [j8]Yuzhao Zhang, Xibing He, Jingchen Zhai, Beihong Ji, Viet Hoang Man, Junmei Wang:
In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. Briefings Bioinform. 22(6) (2021) - [j7]Beihong Ji, Xibing He, Yuzhao Zhang, Jingchen Zhai, Viet Hoang Man, Shuhan Liu, Junmei Wang:
Incorporating structural similarity into a scoring function to enhance the prediction of binding affinities. J. Cheminformatics 13(1): 11 (2021) - 2020
- [j6]Dongxiao Hao, Xibing He, Beihong Ji, Shengli Zhang, Junmei Wang:
How Well Does the Extended Linear Interaction Energy Method Perform in Accurate Binding Free Energy Calculations? J. Chem. Inf. Model. 60(12): 6624-6633 (2020) - 2019
- [j5]Xibing He, Viet Hoang Man, Beihong Ji, Xiang-Qun Xie, Junmei Wang:
Calculate protein-ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3. J. Comput. Aided Mol. Des. 33(1): 105-117 (2019) - [j4]Haixia Ge, Yuemin Bian, Xibing He, Xiang-Qun Xie, Junmei Wang:
Significantly different effects of tetrahydroberberrubine enantiomers on dopamine D1/D2 receptors revealed by experimental study and integrated in silico simulation. J. Comput. Aided Mol. Des. 33(4): 447-459 (2019) - 2017
- [j3]Meagan C. Small, Asaminew H. Aytenfisu, Fang-Yu Lin, Xibing He, Alexander D. MacKerell Jr.:
Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates. J. Comput. Aided Mol. Des. 31(4): 349-363 (2017) - 2014
- [j2]Hui Xing, Hongbin Chen, Xibing He:
Exact multiplicity and stability of solutions of second-order Neumann boundary value problem. Appl. Math. Comput. 232: 1104-1111 (2014) - 2012
- [j1]Wenbo Yu, Xibing He, Kenno Vanommeslaeghe, Alexander D. MacKerell Jr.:
Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations. J. Comput. Chem. 33(31): 2451-2468 (2012)
Coauthor Index
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