Publications by authors named "Xibing He"

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Aberrant S293 Phosphorylation Drives Oligomerization of Tau Repeat R2: Insights from Molecular Dynamics Simulations.
Viet Hoang Man, Xibing He, Phuong H Nguyen, Jie Gao, Junmei Wang

ACS Chem Neurosci· November 2025

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A Full-Spectrum Generative Lead Discovery (FSGLD) Pipeline via DRUG-GAN: A Multiscale Method for Drug-like/Target-specific Compound Library Generation.
Beihong Ji, Matthew Brock, Yuhui Wu, Yuemin Bian, Xibing He

Res Sq· May 2025

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ABCG2: A Milestone Charge Model for Accurate Solvation Free Energy Calculation.
Xibing He, Viet H Man, Wei Yang, Tai-Sung Lee, Junmei Wang

J Chem Theory Comput· March 2025

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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· December 2024

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Geometry Optimization Algorithms in Conjunction with the Machine Learning Potential ANI-2x Facilitate the Structure-Based Virtual Screening and Binding Mode Prediction.
Luxuan Wang, Xibing He, Beihong Ji, Fengyang Han, Taoyu Niu, Jingchen Zhai

Biomolecules· May 2024

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Development and test of highly accurate endpoint free energy methods. 3: partition coefficient prediction using a Poisson-Boltzmann method combined with a solvent accessible surface area model for SAMPL challenges.
Taoyu Niu, Xibing He, Fengyang Han, Luxuan Wang, Junmei Wang

Phys Chem Chem Phys· December 2023

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Predicting anti-SARS-CoV-2 activities of chemical compounds using machine learning models.
Beihong Ji, Yuhui Wu, Elena N Thomas, Jocelyn N Edwards, Xibing He

Artif Intell Chem· December 2023

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In Silico Screening of Natural Flavonoids against 3-Chymotrypsin-like Protease of SARS-CoV-2 Using Machine Learning and Molecular Modeling.
Lianjin Cai, Fengyang Han, Beihong Ji, Xibing He, Luxuan Wang, Jingchen Zhai

Molecules· December 2023

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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

J Chem Inf Model· November 2023

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Unpolarized laser method for infrared spectrum calculation of amide I CO bonds in proteins using molecular dynamics simulation.
Viet Hoang Man, Xibing He, Phuong H Nguyen, Celeste Sagui, Christopher Roland

Comput Biol Med· June 2023

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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 Hoag Man

J Comput Chem· May 2023

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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· May 2023

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Phosphorylation of Tau R2 Repeat Destabilizes Its Binding to Microtubules: A Molecular Dynamics Simulation Study.
Viet Hoang Man, Xibing He, Jie Gao, Junmei Wang

ACS Chem Neurosci· February 2023

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Molecular Modeling Study of a Receptor-Orthosteric Ligand-Allosteric Modulator Signaling Complex.
Chen Jiang, Xibing He, Yuanqiang Wang, Chih-Jung Chen, Yasmin Othman

ACS Chem Neurosci· February 2023

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Phosphorylation at Ser289 Enhances the Oligomerization of Tau Repeat R2.
Viet Hoang Man, Xibing He, Fengyang Han, Lianjin Cai, Luxuan Wang, Jingchen Zhai

J Chem Inf Model· February 2023

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Investigation of the Structure of Full-Length Tau Proteins with Coarse-Grained and All-Atom Molecular Dynamics Simulations.
Xibing He, Viet Hoang Man, Jie Gao, Junmei Wang

ACS Chem Neurosci· January 2023

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Joint Computational/Cell-Based Approach for Screening Inhibitors of Tau Oligomerization: A Proof-of-Concept Study.
Viet Hoang Man, Da Lin, Xibing He, Jie Gao, Junmei Wang

J Alzheimers Dis· September 2022

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binding affinity prediction for metabotropic glutamate receptors using both endpoint free energy methods and a machine learning-based scoring function.
Jingchen Zhai, Xibing He, Yuchen Sun, Zhuoya Wan, Beihong Ji

Phys Chem Chem Phys· August 2022

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Stable Cavitation Interferes with Aβ Oligomerization.
Viet Hoang Man, Xibing He, Junmei Wang

J Chem Inf Model· August 2022

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Recent progress in general force fields of small molecules.
Xibing He, Brandon Walker, Viet H Man, Pengyu Ren, Junmei Wang

Curr Opin Struct Biol· February 2022

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Development and Evaluation of Geometry Optimization Algorithms in Conjunction with ANI Potentials.
Dongxiao Hao, Xibing He, Adrian E Roitberg, Shengli Zhang, Junmei Wang

J Chem Theory Comput· February 2022

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A multiple-step screening protocol to identify allosteric inhibitors of Spike-hACE2 binding.
Jingchen Zhai, Xibing He, Viet Hoang Man, Yuchen Sun, Beihong Ji

Phys Chem Chem Phys· February 2022

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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

Brief Bioinform· November 2021

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Effects of All-Atom Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of PHF6 Peptide of Tau Protein.
Viet Hoang Man, Xibing He, Jie Gao, Junmei Wang

J Chem Theory Comput· October 2021

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Machine learning on ligand-residue interaction profiles to significantly improve binding affinity prediction.
Beihong Ji, Xibing He, Jingchen Zhai, Yuzhao Zhang, Viet Hoang Man

Brief Bioinform· September 2021

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