主讲课程

生物控制论、计算结构信息学导论、生物中的物理化学、生命科学与生物技术概论

个人简介

明灯明，男，1971年11月生，湖北阳新人。1991年～1995年在哈尔滨工业大学应用化学系读本科，1995～1998年在华东理工大学化学系读研究生，1998年～2001年在复旦大学物理系读研究生并获理论物理博士学位。2002年-2008年曾先后在美国贝勒医学院生物化学系、克拉克大学化学系和美国洛斯阿拉莫斯国家实验室计算机与计算科学部从事博士后研究。2009-2016年在复旦大学生命科学学院生理与生物物理系任副研究员。2016年10月至今在全讯白菜策略任职。

主要研究领域为计算结构生物学，包括分子动力学模拟、蛋白质功能预测、蛋白质折叠等。先后在PNAS、PRL、JMB、JCP、Plos One 、Carbohydrate Research 等国际一流权威期刊已经发表了近30篇高质量的学术论文；获得了两项国家自然科学基金面上项目资助。近年来，通过与酶工程实验组合作，从事工程酶的动力学改性设计、催化机制计算机模拟等方面的研究。

代表性成果

1 Xiaokun Wu, Min Han, Dengming Ming^*. Channel dynamics correlations through membrane dynamics: A multi-scale normal mode analysis. J. Chem. Phys. 143, 134113(2015)

2 Yian Yang, Jiaqiang Qian, Dengming Ming^*. Molecular simulation of polysaccharide docking to proteins that have Tryptophan boxes in the binding pockets. Carbohydrate Research 414:78-84 (2015)

3 Yunxiang Sun, Dengming Ming^*. Energetic frustrations in protein folding at residue resolution: a homologous simulation study of Im9 proteins. Plos One. 9:e87719 (2014)

4 Xiongbo An, Xiaokun Wu and Dengming Ming^*. Sequence-based functional sites prediction from a function annotated protein domain profile database. Journal of Fudan University, 52:768-778 (2013)

5 Dengming Ming, Michael E. Wall. Predicting binding sites by analyzing allosteric effects. Methods Molecular Biology. 796:423-36 (2012).

6 Mingyang Lu, Dengming Ming & Jianpeng Ma. fSUB: normal mode analysis with flexible substructures. J Phys. Chem. B, 116:8636-45(2012)

7 Xuehui Chen, Yunxiang Sun, Xiongbo An & Dengming Ming^*.  Virtual interface substructure synthesis method for normal mode analysis of superlarge molecular complexes at atomic resolution. J. Chem. Phys.135:144108 (2011)

8 Judith D. Cohn, Dengming Ming, Michael E. Wall. Prediction of functional sites in 50,000 protein domains using dynamics perturbation analysis. Biophysical Journal. 96:650a, 2009

9 Dengming Ming, Marian Anghel and Michael E. Wall.  Hidden structure in protein energy landscape. Phys. Rev. E. 77:021902 (2008)

10 Dengming Ming, Judith Cohn and Michael E. Wall. Fast dynamics perturbation analysis for prediction of protein functional sites. BMC Struct Biol. 8:5 (2008)

11 Dengming Ming, Michael E. Wall and Kevin Y. Sanbonmatsu. Domain motions in Agonaute, the catalytic engine of RNA interference. BMC Bioinformatics 8:470 (2007)

12 Dengming Ming & Michael E. Wall. Interactions in native binding sites cause a large change in protein dynamics. J. Mol. Biol. 358: 213-23 (2006)

13 Dengming Ming & Michael E. Wall. Allostery in a coarse-grained model of protein dynamics. Phys. Rev. Lett.95:198301. (2005)

14 Dengming Ming & Michael E. Wall. Quantifying allosteric effects in proteins. Proteins. 59: 697-707. (2005)

15 Dengming Ming, Yifei Kong, Yinghao Wu & Jianpeng Ma. Simulation of d-actin filament of several microns. Biophys J. 85:27-35. (2003)

16 Dengming Ming, Yifei Kong, Yinghao Wu and Jianpeng Ma. Substructure Synthesis Methods for Simulating Large Molecular Complexes. Proc. Natl. Acad. Sci. U S A. 100:104-9. (2003).

17 Dengming Ming, Wen Tao, Jixian Dai, W. E. Evenson, Xianxi Dai.  A unified solution of the specific-heat-phonon spectrum inversion problem. Europhys. Lett. 61:723-728. (2003)

18 Dengming Ming, Yifei Kong, Maxime A. L., Zhong Huang and Jianpeng Ma. How to Describe Protein Movements without amino acids sequence and coordinates. Proc. Natl. Acad. Sci. U S A. 99:8620-5. (2002).

19      Dengming Ming, Yifei Kong, Salih J. Wakil and Jiangpeng Ma. Domain Movements in Human Fatty Acid Synthase. Proc. Natl. Acad. Sci. U S A. 99:7895-9. (2002)

20 Dengming Ming, Wen Tao, Jixian Dai, W. E. Evenson, Xianxi Dai.

Generalized emissivity inverse problem. Phys. Rev. E. 65: 045601.

21 Dengming Ming, Wen Tao, Jixian Dai, W. E. Evenson, Xianxi Dai. Exact Solution of the Specific Heat-Phonon Spectrum Problem by Using the Möbius Inversion Formula. Phys. Rev. E. 62: R3019. (Rapid Communications 2000)