分子模拟与设计研究组|Laboratory of Molecular Modeling and Design
 

项目成果

  科研项目

  • 国家重点基础研究发展计划微生物药物创新与优产的人工合成体系【2012CB721000】,2012.1.1-2016.12.31
  • 863计划:面向异构超级计算机的新型蛋白质折叠算法的发展及其应用2012AA01A305】, 2012.1-2015.12
  • 国家自然科学基金青年基金:离子液体对蛋白质结构、动力学特性及其功能影响机理的多尺度模拟【21103168】,2012.1.1-2014.12.31
  • 国家自然科学基金面上项目:结合多尺度相互作用势和分子碎片生长方案的蛋白质功能 预测新理论方法研究【31070641】,2011.1.1-2013.12.31
  • 中国科学院“百人计划”择优支持:针对复杂分子体系的新型理论计算方法的发展及其应用,2011.1.1-2013.12.31
  • 863计划:针对生物医药行业的大规模并行应用软件系统【2009AA01A137】,2010.1.1-2010.12.31
  • 中国科学院外籍专家研究员计划:2010.4.1-2010.7.31

  论        文

 

2012年发表论文

 

50*

Beisi Xu,Dustin E,Yongmei Wang,Haojun Liang,Li GH. A Structural-Based Strategy for Recognition of Transcription Factor Binding Sites. PLOS ONE available online at http://dx.plos.org/10.1371/journal.pone.0052460

49

Liu Zhen,Li Yan,Ren Hong,Zhang Shuwei,Wang Yonghua,Li GH,Ling Yang Structure Requirements for 4-Aryl-4H-Chromenes as Apoptosis Inducers Using 3D QSAR Methods and Docking Studies. Asian Journal of Chenistry;Vol.24,No.6(2012),2450-2460

48

Li Yan,Hao Ming,Ren Hong,Zhang Shuwei,Wang Xia,Ma Ming,Li GH,Ling Yang. Exploring the structure requirement for KC theta inhibitory activity of pyridinecarbonitrile derivatives: an in silico analysis. Journal of Molecular Graphics and Modelling 34 (2012) 76–88

47

Shen HJ, Hricko Patrick J., Colina Coray M., Scott T. Milner. AChiral elasticity of DNA. Soft Matter, 2012, 8, 10090

46*

Ting Fu, Min Hanyi, Xu Yong ,Chen Jianzhong ,Li GH*. Molecular Dynamic Simulation Insights into the Normal State and Restoration of p53 Function. Int. J. Mol. Sci. 2012, 13, 9709-9740; doi:10.3390/ijms13089709

45

Liu Jianling,Liu Mengmeng, Yao Yao,Wang Jinan,Li Yan, Li GH,Wang Yonghua. Identification of Novel Potential beta-N-Acetyl-D-Hexosaminidase Inhibitors by Virtual Screening, Molecular Dynamics Simulation and MM-PBSA Calculationss. Int. J. Mol. Sci. 2012, 13, 4545-4563; doi:10.3390/ijms13044545

44

Zhang Hong, Yao Yao,Yang Huibin, Wang Xia, Kang Zhuo,Li Yan,Li GH,Wang Yonghua. Molecular dynamics and free energy studies on the carboxypeptidases complexed with peptide/small molecular inhibitor: Mechanism for drug resistance. Insect Biochemistry and Molecular Biology 42 (2012) 583e595

43

Zhang Dapeng,Shen HJ,Li GH,Zhao Bailin,Yu Anchi,Zhao Qiang,Wang Hailin. Specific and Sensitive Fluorescence Anisotropy Sensing of Guanine-Quadruplex Structures via a Photoinduced Electron Transfer Mechanism. Anal. Chem. 2012, 84, 8088−8094

42*

Ming Hao, Hong Ren, Fang Luo, Shuwei Zhang, Jieshan Qiu , Mingjuan Ji,Hongzong Si , and Li GH*. A Computational Study on Thiourea Analogs as Potent MK-2 Inhibitors. Int. J. Mol. Sci. 2012, 13, 7057-7079; doi:10.3390/ijms13067057

41

JunPeng Qi, Kun Zhang, Qiao Zhang, Yi Sun, Ting Fu, GuoHui Li and JianFeng Chen. Identification, Characterization and Epitope Mapping of a Human Monoclonal Antibody J19 that Specifically Recognizes the Activated Integrin α4β7. JBC Papers in Press. Published on March 14, 2012 as Manuscript M112.341263

40

Wei-yuan Cheng, Jian-zhong Chen,, Zhi-qiang Liang, Guo-hui Li, Chang-hong Yi, Wei Wang, Ke-yan Wang. A computational analysis of interaction mechanisms of peptide and non-peptide inhibitors with MDMX based on molecular dynamics simulation. W.-y. Cheng et al., Comput. Theoret. Chem. (2012), doi:10.1016/j.comptc.2012.01.010

39*

Jianzhong Chen,Dinglin Zhang, Yuxin Zhang, Li GH*. Computational Studies of Difference in Binding Modes of Peptide and Non-peptide inhibitors to MDM2/MDMX Based on Molecular Dynamics Simulation. International Journal of Molecular Science, 13:2176-2195 
38*
Chu HY, Wang JA, Shen HJ, Yang YL, Zhu WL, Li GH*. Investigation of Family 18 Chitinases and Inhibitors by Computer-aided Approaches. Current Drug Targets, Volume 13, No. 4, April 2012
37
Yongjin J. Zhou, Wei Gao, Qixian Rong, Guojie Jin, Huiying Chu, Wujun Liu,Wei Yang, Zhiwei Zhu, Guohui Li, Guofeng Zhu, Luqi Huang,and Zongbao K. Zhao.Modular Pathway Engineering of Diterpenoid Synthases and the Mevalonic Acid Pathway for Miltiradiene Production. J. Am. Chem. Soc. 2012, 134, 3234−3241

2011年发表论文

36
Hongbo Liu, Xia Wang, Jian Wang, Jinghui Wang, Yan Li, Ling Yang and Li GH.Structural Determinants of CX-4945 Derivatives as Protein Kinase CK2 Inhibitors: A Computational Study. International Journal of Molecular Sciences, 12:7004-7021
35
Ming Hao, Xiaole Zhang, Hong Ren, Yan Li, Shuwei Zhang , Fang Luo ,Mingjuan Ji , Li GH and Ling Yang . In Silico Identification of Structure Requirement for Novel Thiazole and Oxazole Derivatives as Potent Fructose 1,6-Bisphosphatase Inhibitors. International Journal of Molecular Sciences, 12:8161-8180
34
Pingping Bao, Xiaole Zhang, Hong Ren, Yan Li,Zulin Mu, Shuwei Zhang, Li GH and Ling Yang . Structural Requirements of N-Substituted Spiropiperidine Analogues as Agonists of Nociceptin/Orphanin FQ Receptor. International Journal of Molecular Sciences, 12:8961-8981
33*
Chong Xing, Hui Sun, Junmin Zhang, Guohui Li*, Yonggui Robin Chi*. Brønsted Acid Catalyzed α-Alkylation of Aldehydes with Diaryl Methyl Alcohols. Chemistry - A European Journal, 17(44): 12272-12275
32*
Wu J, Xia Z, Shen HJ, Li GH*, Ren PY. Gay-Berne and Electrostatic Multipole based Coarse Grained Model and Application with Polyalanine in Implicit Solvent. Journal of Chemical Physics, 135:155104
31*
Xu BS, Shen HJ, Zhu X, Li GH*. Fast and Accurate Computation Scheme for Vibrational Entropy of Proteins. Journal of Computational Chemistry, 32(15):3188-3193
30*
Jianzhong Chen, Jinan Wang, Xu BS, Zhu WL, Li GH*. Insight into mechanism of small molecule inhibitors of the MDM2-p53 interaction: Molecular dynamics simulation and free energy analysis. Journal of Molecular Graphics and Modeling, 30:46-53
29*
Wang J, Zhu W, Li GH*, Hansmann UH.Velocity-scaling optimized replica exchange molecular dynamics of proteins in a hybrid explicit /implicit solvent. Journal of Chemical Physics 135(8):084115
28*
Ma Hong; Fu Ting; Li GH*. Computational studies on drug-drug interactions and drug-metabolism enzyme interactions. 4th Asia Pacific Meeting of the International-Society-for-the-Study-of -Xenobiotics (ISSX), APR 22-25, 2011 Tainan TAIWAN. Drug Metabolism Reviews(43): 62-63(2011)
27*
许佩军,唐媛媛,张静,张知博,王昆,邵颖,沈虎峻,毛英臣。基于粗粒化模型对有机溶剂的分子动力学模拟,物理化学学报Acta Phys. -Chim. Sin.2011, 27 (X), 001-009

2010年发表论文

26
Qin GR, Yu KQ, Shi T, Luo C, Li GH, Zhu WL, Jiang JL. How Does Influenza Virus A Escape from Amantadine? Journal of Physical Chemistry B, 114 ( 25): 8487-8493 (2010).
25
Liang SC, Ge GB, Liu HX, Zhang YY, Wang LM, Zhang JW, Yin L,Li W, Fang ZZ, Wu JJ, Li GH, Yang L. Identification and Characterization of Human UDP-Glucuronosyltransferases Responsible for the In Vitro Glucuronidation of Daphnetin. Drug Metabolism and Disposition, 38( 6) : 973-980( 2010)

2009年发表论文

24
Xin Li, Jing Guan, Danhong Zhou, Li GH, Xiuwen Han, Weiping Zhang, Xinhe Bao. A DFT study of olefin metathesis over heterogeneous Mo/HBeta catalyst: The influence of Mo oxidation state. Journal of Molecular Structure: THEOCHEM, 913:167-172
23*
Dong PP, Ge GB, Zhang YY, Ai CZ, Li GH*, Zhu LL, Luan HW, Liu XB, Yang L. Quantitative structure- retention relationship studies for taxanes including epimers and isomeric metabolites in ultra fast liquid chromatography, JOURNAL OF CHROMATOGRAPHY A, 1216(42): 7055-7062(2009)

国外工作期间发表论文

22
Jiao D, Zhang JJ, Duke RE, Li GH, Schnieders MJ, Ren PY. Trypsin-Ligand Binding Free Energies from Explicit and Implicit Solvent Simulations with Polarizable Potential. JOURNAL OF COMPUTATIONAL CHEMISTRY, 30(11): 1701 – 1711(2009)
21
Jordan JL, Arndt JW, Hanf K, Li GH, Hall J, Demarest S, Huang F (Huang, Flora)3, Wu XF, Miller B, Glaser S, Fernandez EJ, Wang DP, Lugovskoy A. Structural understanding of stabilization patterns in engineered bispecific Ig-like antibody molecules. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 77(4): 832 – 841(2009)
20
Min DH, Li HZ, Li GH, Berg BA, Fenley MO, Yang W. Efficient sampling of ion motions in molecular dynamics simulations on DNA: Variant Hamiltonian replica exchange method. CHEMICAL PHYSICS LETTERS, 454(4-6): 391-395(2008)
19
Min DH, Li HZ, Li GH, Bitetti-Putzer R, Yang W. Synergistic approach to improve "alchemical" free energy calculation in rugged energy surface. JOURNAL OF CHEMICAL PHYSICS, 126(14): 144109 (2007)
18
Li HZ, Li GH, Berg BA, Yang W. Finite reservoir replica exchange to enhance canonical sampling in rugged energy surfaces. JOURNAL OF CHEMICAL PHYSICS, 125(14), 144902(2006)
17
Riccardi D, Schaefer P, Yang Y, Yu HB, Ghosh N, Prat-Resina X, Konig P, Li GH, Xu DG, Guo H, Elstner M, Cui Q. Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes. JOURNAL OF PHYSICAL CHEMISTRY B, 110: 6458-6469 (2006)
16
Li GH, Cui Q. Direct determination of reaction path and saddle points on the potential of mean force surface. JOURNAL OF MOLECULAR GRAPHICS AND MODELLING, 24(2):82-93(2005)
15
Van Wynsberghe A, Li GH, Cui Q. Normal mode analysis suggests protein flexibility modulation throughout RNA polymerase's functional cycle. BIOCHEMISTRY, 43 (41): 13083-13096 (2004)
14
Cui Q, Li GH, Ma JP, Karplus M. A normal mode analysis of structural plasticity in the biomolecular motor F1-ATPase. JOURNAL OF MOLECULAR BIOLOGY, 340 (2): 345-372(2004)
13
Riccardi D, Li GH, Cui Q. Importance of van der Waals Interactions in QM/MM Simulations. JOURNAL OF PHYSICAL CHEMISTRY B, 108 (20): 6467-6478(2004)
12
Li GH, Cui Q. Mechanochemical coupling in myosin: A theoretical analysis with molecular dynamics and combined QM/MM reaction path calculations. JOURNAL OF PHYSICAL CHEMISTRY B, 108 (10): 3342-3357(2004)
11
Li GH, Cui Q. Analysis of functional motions in Brownian molecular machines with an efficient block normal mode approach: Myosin-II and Ca2+ATPase. BIOPHYSICAL JOURNAL, 86 (2): 743-763(2004)
10
Li GH, Cui Q. pK(a) calculations with QM/MM free energy perturbations. JOURNAL OF PHYSICAL CHEMISTRY B, 107 (51): 14521-14528(2003)
9
Li GH, Cui Q. What is so special about Arg 55 in the catalysis of cyclophilin A? Insights from hybrid QM/MM simulations. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 125 (49): 15028-1503(2003)
8
Li GH, Zhang XD, Cui Q. Free energy perturbation calculations with combined QM/MM Potentials complications, simplifications, and applications to redox potential calculations. JOURNAL OF PHYSICAL CHEMISTRY B, 107 (33): 8643-8653(2003)
7
Li GH, Cui Q. Molecular simulations of conformational dynamics of macromolecular assembly. BIOPHYSICAL JOURNAL, 84(2): 360A-360A(2003)
6
Li GH, Cui Q. A coarse-grained normal mode approach for macromolecules: An efficient implementation and application to Ca2+ATPase. BIOPHYSICAL JOURNAL, 83 (5): 2457-2474 (2002)
5
Xu DG, Li GH, Xie DQ, Guo H. Full-dimensional quantum calculations of vibrational energy levels of acetylene (HCCH) up to 13,000 cm(-1). CHEMICAL PHYSICS LETTERS, 365 (5-6): 480-486(2002)
4
Li GH, Guo H. The vibrational level spectrum of H2O((X)over-tilde(1)A ') from the Partridge-Schwenke potential up to the dissociation limit. JOURNAL OF MOLECULAR SPECTROSCOPY, 210 (1): 90-97 (2001)
3
Li SM, Li GH, Guo H. A single Lanczos propagation method for calculating transition amplitudes. III. S-matrix elements with a complex-symmetric Hamiltonian. JOURNAL OF CHEMICAL PHYSICS, 115 (21): 9637-9643 (2001)
2
Li GH, Guo H. Efficient calculation of resonance positions and widths using doubled Chebyshev autocorrelation functions. CHEMICAL PHYSICS LETTERS, 347 (4-6): 443-450 (2001)
1
Li GH, Guo H. Doubling of Chebyshev correlation function for calculating narrow resonances using low-storage filter diagonalization. CHEMICAL PHYSICS LETTERS, 336 (1-2): 143-148 (2001)

 

  专利及软件著作权

  1. 申请中专利:基于结构的、结合统计势以及分子碎片生长方案的全新蛋白质功能预测及生物大分子设计方法  201010567278.9  中国
  2. 软件著作权:酵母转录因子结合位点预测软件 2011SR053383 中国
  3. 软件著作权:基于统计势的分子碎片生长方案的全新分子设计方法软件 2011SR042206 中国
  4. 申请中专利:基于可极化力场以及pso优化的蛋白质设计方法 201210563431.X中国
  5. 申请中专利:基于三维空间静电势重构的新型蛋白质粗粒化计算方法 201210563541.6中国
  6. 申请中著作权:PSO可极化力场蛋白质设计软件  2012R11S119664  中国
  7. 申请中著作权:backbone_dependent可极化力场蛋白质设计软件 2012R11S119656   中国

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