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All papers authored by Xiangyu Jia

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2019 Xiangyu Jia

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Solvation Free Energy Calculations: The Combination between the Implicitly Polarized Fixed‐charge Model and the Reference Potential Strategy

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2018 Pengfei Li, Xiangyu Jia

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, Xiaoliang Pan

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, Ye Mei

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Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. I. Weighted Thermodynamics Perturbation

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Pengfei Li, Fengjiao Liu, Xiangyu Jia

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, Yihan Shao, Wenxin Hu, Jun Zheng, Ye Mei

Efficient Computation of Free Energy Surfaces of Diels–Alder Reactions in Explicit Solvent at Ab Initio QM/MM Level

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2017 Peng-Fei Li, Xiang-Yu Jia

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, Mei-Ting Wang, Ye Mei

Comparison of Accuracy and Convergence Rate between Equilibrium and Nonequilibrium Alchemical Transformations for Calculation of Relative Binding Free Energy

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Meiting Wang, Pengfei Li, Xiangyu Jia

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, Wei Liu, Yihan Shao

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, Wenxin Hu, Jun Zheng, Bernard R. Brooks, Ye Mei

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Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level

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Wei Liu, Xiangyu Jia

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, Meiting Wang, Pengfei Li, Xiaohui Wang, Wenxin Hu, Jun Zheng, Ye Mei

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Calculations of the absolute binding free energies for Ralstonia solanacearum lectins bound with methyl-α-l-fucoside at molecular mechanical and quantum mechanical/molecular mechanical levels

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2016 Xiangyu Jia

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, Meiting Wang, Yihan Shao, Gerhard König

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, Bernard R. Brooks, John Z. H. Zhang, Ye Mei

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Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics

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2015 Xiangyu Jia

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, Ye Mei

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, John Z. H. Zhang, Yan Mo

Hybrid QM/MM study of FMO complex with polarized protein-specific charge

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2014 Lirong Mou, Xiangyu Jia

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, Ya Gao, Yongxiu Li, John Z. H. Zhang, Ye Mei

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Folding simulation of Trp-cage utilizing a new AMBER compatible force field with coupled main chain torsions

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Xiangyu Jia

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, Juan Zeng, John Z. H. Zhang, Ye Mei

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Accessing the applicability of polarized protein-specific charge in linear interaction energy analysis

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2013 Juan Zeng, Xiangyu Jia

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, John Z. H. Zhang, Ye Mei

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The F130L mutation in streptavidin reduces its binding affinity to biotin through electronic polarization effect

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Xiangyu Jia

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, John Z. H. Zhang, Ye Mei

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Assessing the accuracy of the general AMBER force field for 2,2,2-trifluoroethanol as solvent

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Xiangyu Jia

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, Xianwei Wang, Jinfeng Liu, John Z. H. Zhang, Ye Mei

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, Xiao He

An improved fragment-based quantum mechanical method for calculation of electrostatic solvation energy of proteins

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