Shiji Zhao | Ray Luo Lab

Shiji Zhao

PhD Student

University of California, Irvine

Shiji Zhao works in the Luo Lab with a background in Computer Science.

Publications (13)

Publications listed in the lab bibliography, across all years.

2024

Shiji Zhao, Piotr Cieplak, Yong Duan, Ray Luo (2024). Assessment of Amino Acid Electrostatic Parametrizations of the Polarizable Gaussian Multipole Model. Journal of Chemical Theory and Computation.

2023

Qiang Zhu, Yongxian Wu, Shiji Zhao, Piotr Cieplak, Yong Duan, Ray Luo (2023). Streamlining and Optimizing Strategies of Electrostatic Parameterization. Journal of Chemical Theory and Computation.

Zhen Huang, Shiji Zhao, Piotr Cieplak, Yong Duan, Ray Luo, Haixin Wei (2023). Optimal Scheme to Achieve Energy Conservation in Induced Dipole Models. Journal of Chemical Theory and Computation.

Shiji Zhao, Piotr Cieplak, Yong Duan, Ray Luo (2023). Transferability of the Electrostatic Parameters of the Polarizable Gaussian Multipole Model. Journal of Chemical Theory and Computation.

Hongchao Ji, Xue Lu, Shiji Zhao, Qiqi Wang, Bin Liao, Ludwig G. Bauer, Kilian v. M. Huber, Ray Luo, Ruijun Tian, Chris Soon Heng Tan (2023). Target deconvolution with matrix-augmented pooling strategy reveals cell-specific drug-protein interactions. Cell Chemical Biology.

2022

Shiji Zhao, Haixin Wei, Piotr Cieplak, Yong Duan, Ray Luo (2022). PyRESP : A Program for Electrostatic Parameterizations of Additive and Induced Dipole Polarizable Force Fields. Journal of Chemical Theory and Computation.

Shiji Zhao, Haixin Wei, Piotr Cieplak, Yong Duan, Ray Luo (2022). PyRESP: A flexible program for polarizable force field parameterizations. Biophysical Journal.

Hongchao Ji, Xue Lu, Shiji Zhao, Qiqi Wang, Liao Bin, Kilian v. M. Huber, Ray Luo, Ruijun Tian, Chris Soon Heng Tan (2022). Matrix-Augmented Pooling Strategy for High-Throughput Target Deconvolution Reveals Cell Type Specific Off-Targets and Responses. SSRN Electronic Journal.

Shiji Zhao, Haixin Wei, Piotr Cieplak, Yong Duan, Ray Luo (2022). Accurate Reproduction of Quantum Mechanical Many-Body Interactions in Peptide Main-Chain Hydrogen-Bonding Oligomers by the Polarizable Gaussian Multipole Model. Journal of Chemical Theory and Computation.

2021

Shiji Zhao, Andrew J. Schaub, Shiou-Chuan Tsai, Ray Luo (2021). Development of a Pantetheine Force Field Library for Molecular Modeling. Journal of Chemical Information and Modeling.

2020

Shiji Zhao, Fanglue Ni, Tianyin Qiu, Jacob Wolff, Shiou-Chuan Tsai, Ray Luo (2020). Molecular Basis for Polyketide Ketoreductase–Substrate Interactions. International Journal of Molecular Sciences.

2019

Rebecca E Vargas, Vy Thuy Duong, Han Han, Albert Paul Ta, Yuxuan Chen, Shiji Zhao, Bing Yang, Gayoung Seo, Kimberly Chuc, Sunwoo Oh, Amal El Ali, Olga v Razorenova, Junjie Chen, Ray Luo, Xu Li, Wenqi Wang (2019). Elucidation of WW domain ligand binding specificities in the Hippo pathway reveals STXBP4 as YAP inhibitor. The EMBO Journal.

Andrew J. Schaub, Gabriel O. Moreno, Shiji Zhao, Hau v. Truong, Ray Luo, Shiou-Chuan Tsai (2019). Computational structural enzymology methodologies for the study and engineering of fatty acid synthases, polyketide synthases and nonribosomal peptide synthetases. Methods in Enzymology.