Extensive Assessment of Various Computational Methods for Aspartate's pKa Shift. - Zhaoxi Sun; Xiaohui Wang; Jianing Song (J. Chem. Inf. Model., 2017)

Protein-Ligand Empirical Interaction Components for Virtual Screening. - Yuna Yan; Weijun Wang; Zhaoxi Sun; John Z. H. Zhang; Changge Ji (J. Chem. Inf. Model., 2017)

Model-based process design of a ternary protein separation using multi-step gradient ion-exchange SMB chromatography. - Qiao-Le He; Zhaoxi Sun; Liming Zhao (CoRR, 2019)

BAR-based optimum adaptive steered MD for configurational sampling. - Xiaohui Wang; Xingzhao Tu; Boming Deng; John Z. H. Zhang; Zhaoxi Sun (J. Comput. Chem., 2019)

Determination of Base-Flipping Free-Energy Landscapes from Nonequilibrium Stratification. - Xiaohui Wang; Zhaoxi Sun (J. Chem. Inf. Model., 2019)

Model-based process design of a ternary protein separation using multi-step gradient ion-exchange SMB chromatography. - Qiao-Le He; Eric von Lieres; Zhaoxi Sun; Liming Zhao (Comput. Chem. Eng., 2020)

SAMPL6 host-guest binding affinities and binding poses from spherical-coordinates-biased simulations. - Zhaoxi Sun; Qiao-Le He; Xiao Li; Zhengdan Zhu (J. Comput. Aided Mol. Des., 2020)

Clustering-based convergence diagnostic for multi-modal identification in parameter estimation of chromatography model with parallel MCMC. - Yue-Chao Zhu; Zhaoxi Sun; Qiao-Le He (CoRR, 2021)

SAMPL7 TrimerTrip host-guest binding affinities from extensive alchemical and end-point free energy calculations. - Zhe Huai; Huaiyu Yang; Xiao Li; Zhaoxi Sun (J. Comput. Aided Mol. Des., 2021)

Binding thermodynamics and interaction patterns of human purine nucleoside phosphorylase-inhibitor complexes from extensive free energy calculations. - Zhe Huai; Huaiyu Yang; Zhaoxi Sun (J. Comput. Aided Mol. Des., 2021)

SAMPL7 TrimerTrip host-guest binding poses and binding affinities from spherical-coordinates-biased simulations. - Zhaoxi Sun (J. Comput. Aided Mol. Des., 2021)

Binding Thermodynamics and Interaction Patterns of Inhibitor-Major Urinary Protein-I Binding from Extensive Free-Energy Calculations: Benchmarking AMBER Force Fields. - Zhe Huai; Zhaoxi Shen; Zhaoxi Sun (J. Chem. Inf. Model., 2021)

A General Picture of Cucurbit[8]uril Host-Guest Binding. - Zhaoxi Sun; Zhe Huai; Qiao-Le He; Zhirong Liu (J. Chem. Inf. Model., 2021)

Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: II. regression and dielectric constant. - Xiao Liu; Lei Zheng; Yalong Cong; Zhihao Gong; Zhixiang Yin; John Z. H. Zhang; Zhirong Liu; Zhaoxi Sun (J. Comput. Aided Mol. Des., 2022)

Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: I. Standard procedure. - Xiao Liu; Lei Zheng; Chu Qin; John Z. H. Zhang; Zhaoxi Sun (J. Comput. Aided Mol. Des., 2022)

Screening Power of End-Point Free-Energy Calculations in Cucurbituril Host-Guest Systems. - Xiao Liu; Lei Zheng; Chu Qin; Yang Li 123; John Z. H. Zhang; Zhaoxi Sun (J. Chem. Inf. Model., 2023)