National Science Foundation Presidential Faculty Fellow
Camille Dreyfus Teacher-Scholar
Alfred P. Sloan Research Fellow
Overseas Assessor of Chinese Academy of Science
国家重大人才工程专家
第六届中国侨界贡献奖
英国皇家化学会Fellow
（科研成果）重大科技项目承担情况，代表性文章、成果转化情况
重大科技项目承担情况：
1)上海市浦江人才计划，50万，2009-2012.
2)基金委重点项目，“生物大分子的高效率量子化学分块计算方法和蛋白质极化电荷”（PI），160万，2010-2013.
3)基金委重点项目，“蛋白质动力学的多层次理论计算方法与应用”（PI），320万，2015-2019.
4)国家重点研发专项，“蛋白-蛋白相互作用及其网络的理论计算新方法与应用”（首席），1,782万，2016-2021.
5)基金委重点项目，“复杂生物体系介观尺度动态结构与相互作用的理论计算化学研究”（Co-PI），173万，2020-2024.
6）基金委重点项目，“生物大分子的高效率量子化学分块计算方法和蛋白质极化电荷”（PI），160万，2010-2013.
7）基金委外国资深学者项目，“酶催化的智能设计与模拟”（PI），160万，2022-2023.
8）基金委重点项目，“基于量子化学精度的蛋白-配体相互作用的理论计算模拟”（PI），230万，2024-2028.
专利：
1. Dawei Zhang and John Zeng Hui Zhang, “A METHOD FOR INTRODUCING CONJUGATED CAPS ONTO MOLECULAR FRAGMENTS AND SYSTEMS AND METHODS FOR USING THE SAME TO DETERMINE INTER-MOLECULAR INTERACTION ENERGIES”, Patent No.: US 7,729,867 B2, Date of Patent: Jun. 1, 2010.
2. LEEHUANG S; LIN H P; ZHANG D; ZHANG J Z H; CHANG Y T; LEE J W; BAO J; SUN Y; HUANG P L, “Compositions and methods for treating obesity, obesity related disorders and for inhibiting the infectivity of human immunodeficiency virus”, US9132145-B2, September. 15, 2015.
3.何晓，刘金峰，张增辉，“一种非核苷类HIV-1反转录酶抑制剂”,专利号201310242563.7，Nov. 18, 2015
4.季长鸽，闫玉娜，张增辉，“基于相互作用指纹和机器学习的药物靶标的虚拟筛选方法”，专利号：201610852817.0，Nov. 9, 2018.
5.潘月，张鲁嘉，张增辉，何晓，张传玺，方波欢，“一种基于酵母二肽基肽酶Ⅲ的抗体模拟物及其应用”，专利号：ZL 202010192357.X，2020年10月20。
6.赵玥，张鲁嘉，张增辉，何晓，方波欢，“一种基于α螺旋融合两种蛋白质且保持各自亚基活性的蛋白质融合设计方法”，专利号：202010192367.3, 2020年3月18。
7.赵玥，张鲁嘉，张增辉，韩艳芳，何晓，方波欢，“一种表达微管β亚基与蛋白A的D结构域融合蛋白的基因工程菌株及其构建方法”，专利号：202010207523.9，2020年3月23。
代表性论文：
1.D.H. Zhang andJ.Z.H. Zhang, “Full-dimensional time-dependent treatment for diatom-diatom reactions: the H2 + OH reaction,”J. Chem. Phys. 101, 1146 (1994). 1998-08-31
2.D.W. Zhang andJ.Z.H. Zhang, “Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein-molecule interaction energy”,J. Chem. Phys.119, 3599 (2003).
3.C.G. Ji, Y. Mei andJ.Z.H. Zhang, “Developing polarized protein-specific charges for protein dynamics: MD free energy calculation of pKa shifts for Asp26/Asp20 in thioredoxin”,Biophysical Journal95, 1080 (2008).
4.C.G. Ji andJ.Z.H. Zhang, “Protein Polarization Is Critical to Stabilizing AF-2 and Helix-2’ Domains in Ligand Binding to PPAR gamma”,J. Am. Chem. Soc. 130, 17129–17133 (2008).
5.Y. Tong, C.G. Ji, Y. Mei,J.Z.H. Zhang, “Simulation of NMR Data Reveals that Protein’s local structures Are Stabilized by Electronic Polarization”,J. Am. Chem. Soc.131, 8636–8641 (2009).
6.Y. Tong, Y. Mei, Y.L. Li, C.G. Ji,J.Z.H. Zhang, “Electrostatic polarization makes substantial contribution to free energy of avidin-biotin binding",J. Am. Chem. Soc.132, 5137-5142 (2010).
7.Li L. Duan,Ye Mei,Dawei Zhang, Qing G. Zhang, andJohn Z. H. Zhang, “Folding of a Helix at Room Temperature Is Critically Aided by Electrostatic Polarization of Intraprotein Hydrogen Bonds”,J. Am. Chem. Soc.132, 11159–11164 (2010).
8.C.G. Ji andJ.Z.H. Zhang, “Understanding the Molecular Mechanism of Enzyme Dynamics of Ribonuclease A through Protonation/Deprotonation of HIS48”,J. Am. Chem. Soc. 133, 17727-17737 (2011).
9.Xiao He, Tong Zhu, Xianwei Wang, JInfeng Liu, andJohn Z. H. Zhang, "Fragment quantum mechanical calculation of proteins and its applications"Acc. Chem. Res.47(9) 2748-2757 (2014).
10.L.L. Duan, X. Liu,J.Z.H. Zhang, “Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein–Ligand Binding Free Energy”,J. Am. Chem. Soc., 138, 5722–5728 (2016).
11.Y.N. Yan, M.Y. Yang, C.G. Ji,John Z.H. Zhang, “Interaction Entropy for Computational Alanine Scanning”,J. Chem. Inf. Model.,57, 1112-1122 (2017).
12.Z.X. Sun, Y.N. Yan, M.Y. Yang,John Z.H. Zhang, “Interaction entropy for protein-protein binding”,J. Chem. Phys., 146, 124124 (2017).
13.L.Q. Qiu, Y.N. Yan, Z.X. Sun, J.N. Song,John Z.H. Zhang, “Interaction entropy for computational alanine scanning in protein–protein binding”,WIREs Comput. Mol. Sci., 8, e1342 (2018).
14.E.C. Wang, H.Y. Sun, J.M. Wang, Z. Wang, H. Liu,J.Z.H. Zhang, T.J. Hou, “End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design”,Chem. Rev.,119, 9478−9508 (2019).
15.Jinzhe Zeng, Liqun Cao, Mingyuan Xu, Tong Zhu*,John Z. H. Zhang, Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation,Nature Communications, 11, 5713. (2020).
16.Jingxiao Bao, Xiao He, andJohn Z. H. Zhang, DeepBSP-a Machine Learning Method for Accurate Prediction of Protein−Ligand Docking Structures,J. Chem. Inf. Model., 2021, 61, 2231−2240.
