个人主页：https://www.x-mol.com/groups/tcbioe?lang=zh

教育背景：

2012中科院上海生命科学研究院计算生物学研究所，计算生物学，博士

2009.11-2010.10德国海德堡理论研究所，中欧联合培养博士生

2010.11-2011.12德国马普生物物理化学研究所，中欧联合培养博士生

2004浙江大学材料与化学工程学院，生物工程，学士

工作经历：

2017.9-至今 深圳大学，研究员

2017.3-2017.6中科院大连化学物理研究所，助理研究员

2013.3-2016.12美国伊利诺伊大学芝加哥分校，博士后

2012.10-2013.2德国海德堡理论研究所,博士后

所获奖项：

2018年深圳市海外高层次人才“孔雀计划”C类

2018年深圳市南山区领航人才C类

研究兴趣：

1，生物大分子的结构和功能

主要运用分子动力学模拟技术研究RNA表观遗传和自身免疫疾病相关的重要蛋白在原子水平的作用机理，为药物开发提供理论依据。

2，酶催化反应机理

通过理论计算研究非天然氨基酸对特定酶功能影响的机理以及可能的优化手段。

3、机械化学

研究机械力如何影响化学反应的进程，包括对反应速率和反应产物等的影响。

4、计算机辅助药物发现

主要运用机器学习、分子对接和分子动力学模拟等方法，研究与药物-靶点相关的序列-结构-活性关系。

5、理论计算方法开发

包括增强采样方法、能量分解方法、反应坐标鉴定方法和和多尺度模拟方法开发。

科研项目：

1，广东省基础与应用基础研究基金面上项目，2023.01-2025.12，10万，主持，在研。

2，深圳市高等院校稳定支持计划面上项目，2022.10-2024.09，29万，主持，在研。

3，企业横向项目，2021.06-2023.05，20万，主持，在研。

4，广东省基础与应用基础研究基金面上项目，2019.10-2022.09，10万，主持，结题。

5，深圳大学青年教师-科研启动项目，2019.10-2022.09，20万，主持，结题。

6，深圳市高层次人才启动项目，2019.01-2021.12，270万，主持，结题。

7，国家自然科学基金面上项目，2018.01-2021.12，58万，主持，结题。

课题组成员：

博士后：MUHAMMAD JUNAID，MUHAMMAD FAKHAR

硕士生：朱琳（2020级），Alsam Memoona（2021级）

发表论文：

(详见谷歌学术https://scholar.google.com/citations?user=rkKWAEsAAAAJ&hl=en)

2022

[31]Li W. Optimizing reaction coordinate by flux maximization in the transition path ensemble. The Journal of Chemical Physics, 2022, 156(5): 054117.

[30]Zhu L, Li W. Roles of Physicochemical and Structural Properties of RNA-Binding Proteins in Predicting the Activities of Trans-Acting Splicing Factors with Machine Learning. International Journal of Molecular Sciences, 2022, 23(8): 4426.

[29]Li W. Time-lagged Flux in the Transition Path Ensemble: Flux Maximization and Relation to Transition Path Theory. The Journal of Physical Chemistry A, 2022, 126(23): 3797-3810.

[28]Li W. Energy Decomposition along Reaction Coordinate: Theory and Applications to Nonequilibrium Ensembles of Trajectories. The Journal of Physical Chemistry A, 2022, 126(42): 7763-7773.

[27]Li W. Potential Energy Weighted Reactive Flux and Total Rate of Change of Potential Energy: Theory and Illustrative Applications. The Journal of Physical Chemistry A, 2022, 126(42): 7774-7786.

2021

[26]Wang X, Li W. Comparative Study of Interactions between Human cGAS and Inhibitors: Insights from Molecular Dynamics and MM/PBSA Studies. International Journal of Molecular Sciences, 2021, 22(3): 1164.

[25] Fu Q, Fu C, Teng L, Li W, Sheng Y, Handschuh-Wang, S. Rapid synthesis and growth process deconvolution of Au nanoflowers with ultrahigh catalytic activity based on microfluidics. Journal of Materials Science, 2021, 56: 6315-6326.

[24]Zhu L, Davari M D, Li W. Recent advances in the prediction of protein structural classes: Feature descriptors and machine learning algorithms. Crystals, 2021, 11(4): 324.

[23] Lin L, Zou H, Li W, Xu L Y, Li E M, Dong G. Redox Potentials of Disulfide Bonds in LOXL2 Studied by Nonequilibrium Alchemical Simulation. Frontiers in Chemistry, 2021, 9: 797036.

[22]Singh N, Mao S Q, Li W. Identification of Novel Inhibitors of Type-I Mycobacterium Tuberculosis Fatty Acid Synthase Using Docking-Based Virtual Screening and Molecular Dynamics Simulation. Applied Sciences, 2021, 11(15): 6977.

2020

[21]Wang X, Li W. Development and testing of force field parameters for phenylalanine and tyrosine derivatives. Frontiers in Molecular Biosciences, 2020, 7: 608931.

[20]Wang X, Zhang H, Li W. DNA-binding mechanisms of human and mouse cGAS: A comparative MD and MM/GBSA study. Physical Chemistry Chemical Physics, 2020, 22(45): 26390-26401.

[19] Singh N, Li W. Absolute Binding Free Energy Calculations for Highly Flexible Protein MDM2 and its inhibitors. International journal of molecular sciences, 2020, 21(13): 4765.

[18] Cai M, Liu Y, Yin X, Zhou Z, Friedrich MW, Richter-Heitmann T, Nimzyk R, Kulkarni A, Wang X, Li W, Pan J. Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation. Science China Life Sciences. 2020 Mar 16:1-2.

[17]Gutierrez Moreno J J, Pan K, Wang Y, Li W.Computational Study of APTES Surface Functionalization of Diatom-like Amorphous SiO2 Surfaces for Heavy Metal Adsorption.Langmuir, 2020, 36(20): 5680-5689.

[16] Li W. Residue-Residue Mutual Work Analysis of Retinal-Opsin Interaction in Rhodopsin: Implications for Protein-Ligand Binding, Journal of Chemical Theory and Computation, 2020, 16(3): 1834-1842.

2019

[15] Gutierrez Moreno J J, Fronzi M, Lovera P, O'Riordan A, Ford M, Li W, M Nolan. Structure, stability and water adsorption on ultra-thin TiO2 supported on TiN. Physical Chemistry Chemical Physics, 2019, 21(45): 25344-25361.

[14] Singh N, Li W. Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications. International journal of molecular sciences, 2019, 20(15): 3774.

2018

[13] Li W. Equipartition terms in transition path ensemble: Insights from molecular dynamics simulations of alanine dipeptide. The Journal of chemical physics, 2018, 148(8): 084105.

入职深大前

[12] Li W, Ma A. A benchmark for reaction coordinates in the transition path ensemble. The Journal of chemical physics, 2016, 144(13): 134104.

[11] Li W, Ma A. Reaction mechanism and reaction coordinates from the viewpoint of energy flow. The Journal of chemical physics, 2016, 144(11): 114103.

[10] Li W, Ma A. Some studies on generalized coordinate sets for polyatomic molecules. The Journal of chemical physics, 2015, 143(22): 224103.

[9] Li W, Ma A. Reducing the cost of evaluating the committor by a fitting procedure. The Journal of chemical physics, 2015, 143(17): 174103.

[8] Li W, Baldus I B, Gräter F. Redox potentials of protein disulfide bonds from free-energy calculations. The Journal of Physical Chemistry B, 2015, 119(17): 5386-5391.

[7] Li W, Ma A. Recent developments in methods for identifying reaction coordinates. Molecular simulation, 2014, 40(10-11): 784-793.

[6] Zhou B, Baldus I B, Li W, Edwards SA, Graeter F. Identification of allosteric disulfides from prestress analysis. Biophysical journal, 2014, 107(3): 672-681.

[5] Li W, Edwards SA, Lu L, Kubar T, Patil SP, Grubmueller H, Groenhof G, and Graeter F. Force Distribution Analysis of Mechanochemically Reactive Dimethylcyclobutene. ChemPhysChem, 2013, 14(12): 2687-2697.

[4] Li W, Rudack T, Gerwert K, Graeter F, and Schlitter J. Exploring the Multi-Dimensional Free Energy Surface of Phosphoester Hydrolysis with Constrained QM/MM Dynamics. Journal of chemical theory and computation, 2012, 8(10): 3596-3604.

[3] Li W, Gräter F. Atomistic evidence of how force dynamically regulates thiol/disulfide exchange. Journal of the American Chemical Society, 2010, 132(47): 16790-16795.

[2] Chen L, Lu L, Feng K, Li W, Song J, Zheng L, ... and Cai Y. Multiple classifier integration for the prediction of protein structural classes. Journal of Computational Chemistry, 2009, 30(14): 2248-2254.

[1] Li W, Lin K, Feng K, et al. Prediction of protein structural classes using hybrid properties. Molecular diversity, 2008, 12(3-4): 171-179.

专著章节：

[4] Li W. Mechanophores in Polymer Mechanochemistry: Insights from Single-Molecule Experiments and Computer Simulations.InFunctional Tactile Sensors, Elsevier, 2021: 113-139.

[3] Wang X, Singh N, Li W. Molecular Dynamics Simulation of Biomolecular Interactions. In Systems Medicine: Integrative, Qualitative and Computational Approaches, Elsevier, 2019: 182–189.

[2] Gräter F, Li W. Studying Functional Disulphide Bonds by Computer Simulations. InFunctional Disulphide Bonds. Humana, New York, NY, 2019: 87-113.

[1] Gräter F, Li W. Transition path sampling with quantum/classical mechanics for reaction rates. InMolecular Modeling of Proteins. Humana Press, New York, NY, 2015: 27-45.