David Minh

Education

Ph.D. University of California, San Diego
M.S. University of California, San Diego
B.A. University of California, Berkeley

Research Interests

David Minh小组的研究方向是计算化学生物学. That is, 我们开发和应用计算方法来表征小分子和生物分子之间的相互作用.

More specifically, our current efforts are:

1. 更快和更准确的结合自由能计算方法. Unlike fast molecular docking methods, 我们的新方法考虑了熵和结合焓. 我们推导出新的理论，使严格的束缚自由能计算的计算捷径. 我们还开发和测试了实现新理论的计算机软件.
2. Techniques to enhance sampling in molecular simulations. 模拟不需要模拟原子尺度上的运动，以便从适当的平衡分布中取样配置. We are implementing and testing new types of Monte Carlo moves.
3. 化学计量学方法集成和分析来自多个来源的测量数据. 我们正在编写基于贝叶斯统计(深度学习的基础)的统计分析包，以组合来自多个测量和仪器的绑定相关数据. 该计划还将提出新的实验，以最大限度地获取信息.
4. Application of molecular modeling to biomedical problems. In collaboration with Oscar Juarez from the biology department, 我们目前正专注于对致病菌的代谢酶进行建模. 我们正在研究氧化还原诱导的构象变化以及代谢物和抑制剂的结合. 我们计划筛选和优化新的抑制剂作为潜在的抗生素.

Publications

Menzer, W. M.†, Xie, B. & Minh, D. D. L.*. (2020). 终点蛋白-配体结合自由能计算中的约束. Journal of Computational Chemistry, 41, 573–586.

Minh, D. D. L.*. (2020). 炼金术网格码头(AlGDock):柔性配体和刚性受体之间的结合自由能计算. Journal of Computational Chemistry, 41, 715–730.

Fang, X., Osipiuk, J., Chakravarthy, S., Yuan, M., Menzer, W.†, Nissen, D., Liang, P., Raba, D. A., Tuz, K., Howard, A. J., Joachimiak, A., Minh, D. D. L. & Juarez, O. (2019). 霍乱弧菌黄素转移酶ApbE的动力学和反应机理:保守组氨酸257在催化中的作用. Journal of Biological Chemistry, 294, 13800–13810.

Nguyen, T. H., Ngo, V., Castro Zerba, J.†, Noskov, S. Y. & Minh, D. D. L.*. (2019). Nonequilibrium path-ensemble averages for symmetric protocols. Journal of Chemical Physics, 151, 194103.

Raba, D. A., Yuan, M., Fang, X., Menzer, W.†, Liang, P., Tuz, K., Minh, D. D. L. & Juarez, O. (2019). 亚基D在霍乱弧菌NQR泛素结合位点的作用:口袋灵活性和抑制剂抗性. ACS Omega, 4, 19324–19331.

Xie, B. & Minh, D. D. L.*. (2019). D3R大挑战3中炼金术网格码头(AlGDock)的计算. Journal of Computer-Aided Molecular Design, 33, 61–69.

Menzer, W.†, Li, C., Sun, W., Xie, B. & Minh, D. D. L.*. (2018). Simple Entropy Terms for End-Point Binding Free Energy Calculations. Journal of Chemical Theory and Computation, 14, 6035–6049.

Minh, D. D. L.*. (2018). 功率变换改进了分子力学相互作用能量网格的插值. Journal of Computational Chemistry, 39, 1200–1207.

Nguyen, T. H. & Minh, D. D. L.*. (2018). Implicit ligand theory for relative binding free energies. Journal of Chemical Physics, 148, 104114.4

Nguyen, T. H., Rustenburg, A. S., Krimmer, S. G., Zhang, H., Clark, J. D.†, Novick, P. A., Branson, K., Pande, V. S., Chodera, J. D. & Minh, D. D. L.*. (2018). 结合热力学等温滴定量热的贝叶斯分析. PloS One, 13, e0203224.

Nguyen, T. H., Zhou, H.-X. & Minh, D. D. L.*. (2018). 用快速傅立叶变换计算束缚自由能. Journal of Computational Chemistry, 39, 621–636.

Raba, D. A., Rosas-Lemus, M., Menzer, W. M.†, Li, C., Fang, X., Liang, P., Tuz, K., Minh, D. D. L. & Juárez, O. (2018). Characterization of the Pseudomonas aeruginosa NQR Complex, a Bacterial Proton Pump with Roles in Autopoisoning Resistance. Journal of Biological Chemistry, 293, 15664–15677.

Ren, S., Sun, X., Wang, H., Nguyen, T. H., Sadeghipour, N., Xu, X., Kang, C. S., Liu, Y., Xu, H., Wu, N., Chen, Y., Tichauer, K., Minh, D. D. L. & Chong, H.-S. (2018). Design, Synthesis, 新型聚氨基羧酸配体治疗偶联物用于抗体靶向癌症治疗和近红外光学成像的生物学评价. ChemMedChem, 13, 2606–2617.

Xie, B., Clark, J. D.† & Minh, D. D. L.*. (2018). 使用简化集合对接的分层效率. Journal of Chemical Information and Modeling, 58, 1915–1925.

Onuk, E., Badger, J., Wang, Y. J., Bardhan, J., Chishti, Y., Akcakaya, M., Brooks, D. H.,

Erdogmus, D., Minh, D. D. L. & Makowski, L. (2017). 催化作用和配体结合对腺苷酸激酶构象集合的影响. Biochemistry, 56, 4559–4567.

Spiridon, L. & Minh, D. D. L.*. (2017). 约束分子动力学的哈密顿蒙特卡罗Gibbs采样. Journal of Chemical Theory and Computation, 13, 4649–4659.

Tuz, K., Li, C., Fang, X., Raba, D. A., Liang, P., Minh, D. D. L. & Juárez, O. (2017). 霍乱弧菌钠依赖性NADH脱氢酶催化泛素结合位点的鉴定. Journal of Biological Chemistry, 292, 3039–3048.

Xie, B., Nguyen, T. H. & Minh, D. D. L.*. (2017). T4溶菌酶与141个小分子之间的绝对结合自由能:基于多个刚性受体构型的计算. Journal of Chemical Theory and Computation, 13, 2930–2944.

Minh, D. D. L., Minh, D. L. & Nguyen, A. L. (2016). Layer Sampling. 统计通讯-模拟与计算，45,73-100.

Nguyen, T. H. & Minh, D. D. L.*. (2016). 中间热力学态同样有助于自由能收敛:一个副本交换的证明. Journal of Chemical Theory and Computation, 12, 2154–2161.

Minh DDL, Minh DL, Nguyen L. Layer Sampling, Commun Stat Simulat Comput, in press. doi: 10.1080/03610918.2013.854907

Minh DDL, Minh DL. 对黑斯廷斯算法的理解，公共统计仿真计算，44 (2)，332-349 (2015). doi: 10.1080/03610918.2013.777455

Minh DDL, Makowski L. 广角x射线溶液散射用于蛋白质配体结合:贝叶斯置信区间的多变量曲线分辨率. Biophysical Journal, 104: 873-883 (2013). doi: 10.1016/j.bpj.2012.12.019

Minh DDL. 隐式配体理论:严格的结合自由能和分子对接的热力学期望. J Chem Phys, 137: 104106 (2012). doi:10.1063/1.4751284

Nilmeier JP, Crooks GE, Minh DDL, Chodera JD. 非平衡候选蒙特卡罗是平衡模拟的有效工具, Proc Natl Acad Sci USA, 108(45):E1009-1018 (2011). doi:10.1073/pnas.1106094108

Minh DDL, Vaikuntanathan S. 非平衡路径的密度相关分析改进自由能估计2. A Feynman-Kac Formalism. J Chem Phys, 134(3): 034117 (2011). doi:10.1063/1.3541152

Minh DDL, Chodera JD. 利用驱动非平衡过程的多个时间片估计平衡系综平均:理论和在自由能中的应用, moments, and thermodynamic length in single-molecule pulling experiments. J Chem Phys, 134(2): 024111 (2011). doi:10.1063/1.3516517

Minh DDL. 优化复制气体估计的绝对积分和配分函数. Phys Rev E, 82(3): 031132 (2010). doi:10.1103/PhysRevE.82.031132

Minh DDL, Chodera JD. 非平衡路径-集合平均的最优估计量和渐近方差. J Chem Phys, 131(13): 134110 (2009). doi:10.1063/1.3242285

Minh DDL. 非平衡路径的密度相关分析改进了自由能估计. J Chem Phys, 130(20): 204102 (2009). doi:10.1063/1.3139189

Minh DDL, Adib AB. Path integral analysis of Jarzynski's equality: Analytical results. Phys Rev E, 79(2): 021122 (2009). doi: 10.1103/PhysRevE.79.021122

Minh DDL, Adib AB. 双向单分子力谱优化自由能. Phys Rev Lett, 100(18): 180602 (2008). doi:10.1103/PhysRevLett.100.180602

Amaro R, Minh DDL, Cheng L, Lindstrom WM, Olson AJ, Lin JH, Olson AJ, McCammon JA. 禽流感N1显著的环灵活性及其对抗病毒药物设计的影响. J Am Chem Soc, 129(25):7764-7765 (2007). doi:10.1021/ja0723535

Minh DDL. 不同偏置程序下实验的自由能重建. Phys Rev E, 74(6): 061120 (2006). doi:10.1103/PhysRevE.74.061120

Minh DDL, Chang CE, Trylska J, Tozzini V, and McCammon JA. 大分子拥挤对HIV-1蛋白酶内部动力学的影响. J Am Chem Soc, 128(18): 6006-6007 (2006). doi:10.1021/ja060483s

Minh DDL, Bui JM, Chang CE, Jain T, Swanson JM, McCammon JA. 蛋白质-蛋白质结合的熵成本:乙酰胆碱酯酶与束状蛋白-2结合的案例研究. Biophys J, 89(4):L25-7 (2005). doi:10.1529/biophysj.105.069336

Expertise

• Computational Chemical Biology and Structure-Based Drug Design
• Theoretical Chemistry, especially Statistical Mechanics
• Biophysical Chemistry