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 科研项目

1 理论与计算生物物理化学 400万 2017.1--2021.12 基金委-杰青


2 基于多尺度分子动力学模拟和高精度可极化力场研究PIP2对TRP通道调控的微观分子机理 28.34万 2018.1-- 2020.12 基金委-青年


3非天然氨基酸突变的蛋白酶催化反应机理的理论计算研究 69.6万 2018.1-- 2021.12 基金委-面上


4靶向Fut8的抑制剂筛选及用于治疗IBD(炎症性肠病)的研究 400万 2018.--1 2019.12 大连市支持高层次人才创新创业-高层次人才创新支持计划

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论文题目 作者 刊名或著作名 年份
A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids 楚慧郢,彭向达,李焱,张跃斌,李国辉 MOLECULES 2018


Cholesterol modulating the orientation of His17 in hepatitis C virus p7 (5a) viroporin - A molecular dynamic simulation study 张跃斌,彭向达,Ren Hong,楚慧郢,李焱,李国辉 CHINESE CHEMICAL LETTERS 2018


Y08060: A Selective BET Inhibitor for Treatment of Prostate Cancer Qiuping Xiang, Yan Zhang, Jiaguo Li, Xiaoqian Xue, Chao Wang, Ming Song, Cheng Zhang, Rui Wang, Chenchang Li, Chun Wu, Yulai Zhou, Xiaohong Yang, 李国辉, Ke Ding , Yong Xu ACS Medicinal Chemistry Letters 2018


Benzoxazinone-containing 3,5-dimethylisoxazole derivatives as BET bromodomain inhibitors for treatment of castration-resistant prostate cancer Xiaoqian Xue, Yan Zhang, Chao Wang, Maofeng Zhang, Qiuping Xiang,Junjian Wang, Anhui Wang, Chenchang Li, Cheng Zhang, Lingjiao Zou,Rui Wang,Shuang Wu,Yongzhi Lu,Hongwu Chen,Ke Ding,李国辉 EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY 2018


Single glucose molecule transport process revealed by force tracing and molecular dynamics simulations Pan YG, 张跃斌, Gongpan PC, Zhang QR, Huang ST, Wang B, Xu BQ, Shan YP, Xiong WY, 李国辉, Wang HD NANOSCALE HORIZONS 2018


Macrophage-Associated PGK1 Phosphorylation Promotes Aerobic Glycolysis and Tumorigenesis Yajuan Zhang, Guanzhen Yu,楚慧郢,Xiongjun Wang,Lingling Xiong,Guoqing Cai,Ruilong Liu,Hong Gao,Bangbao Tao,Wenfeng Li,李国辉,Ji Liang, Weiwei Yang MOLECULAR CELL 2018


Integrin alpha 4 beta 7 switches its ligand specificity via distinct conformer-specific activation ShiHui Wang, ChenYu Wu,张跃斌, QingLu Zhong, Hao Sun, WenPeng Cao, GaoXiang Ge,李国辉, X. Frank Zhang,JianFeng Chen JOURNAL OF CELL BIOLOGY 2018


Integrating Multiple Accelerated Molecular Dynamics To Improve Accuracy of Free Energy Calculations 彭向达,张跃斌,李焱,刘庆龙,楚慧郢,张鼎林 Journal of Chemical Theory and Computation 2018


Structural insight into precursor tRNA processing by yeast ribonuclease P Lan Pengfei, Tan Ming, 张跃斌, Niu Shuangshuang, Chen Juan, Shi Shaohua, Qiu Shuwan, Wang Xuejuan, 彭向达, Cai Gang, Cheng Hong, Wu Jian, 李国辉, Lei Ming SCIENCE 2018


Polarizable atomic multipole-based force field for DOPC and POPE membrane lipids 楚慧郢,彭向达,李焱,张跃斌,Hanyi Min,李国辉 MOLECULAR PHYSICS 2018
Intramembrane ionic protein–lipid interaction regulates integrin structure and function Jun GuoID, Youhua Zhang, Hua Li, 楚慧郢, Qinshu Wang, Shutan Jiang,李焱, Hongbin Shen, 李国辉, Jianfeng Chen, Chenqi Xu PLOS BIOLOGY 2018


Higher Accuracy Achieved in the Simulations of Protein Structure Refinement, Protein Folding and Intrinsically Disordered Proteins Using Polarizable Force Fields. 王安徽, Zhang Zhichao, 李国辉 Journal of Physical Chemistry Letters 2018


Exosome cofactor hMTR4 competes with export adaptor ALYREF to ensure balanced nuclear RNA pools for degradation and export Jing Fan, Bin Kuai, Guifen Wu, 吴旭东, Binkai Chi, Lantian Wang, Ke Wang, Zhubing Shi, Heng Zhang, She Chen, Zhisong He, Siyuan Wang, Zhaocai Zhou, 李国辉, Hong Cheng EMBO JOURNAL 2017


ALYREF mainly binds to the 5 and the 3 regions of the mRNA in vivo Min Shi, Heng Zhang, 吴旭东, Zhisong He, Lantian Wang, Shanye Yin, Bin Tian,李国辉 ,Hong Cheng NUCLEIC ACIDS RESEARCH 2017


Polarizable force field development for lipids and their efficient applications in membrane proteins 楚慧郢, 曹了然, 彭向达, 李国辉 Wiley Interdisciplinary Reviews-Computational Molecular Science 2017


Inert Gas Deactivates Protein Activity by Aggregation Lijuan Zhang, 张跃斌, Jie Cheng, Lei Wang, Xingya Wang, Meng Zhang,Yi Gao, Jun Hu, Xuehua Zhang, Junhong Lü, 李国辉, Renzhong Tai, Haiping Fang Scientific Reports 2017


Recent Developments in Using Molecular Dynamics Simulation Techniques to Study Biomolecules 曹了然 ,张春煜,张鼎林,楚慧郢,张跃斌,李国辉 Acta Physico-Chimica Sinica物理化学学报 2017


一种基于分块迭代法的高精度原子电荷计算方法 李焱,汤天宝,金乐,李冬婷,李国辉,许佩军 科研信息化技术与应用 2017


Membrane biophysics Hongda Wang, 李国辉 Membrane Biophysics 2017


Chapter 12 Computer Simulations to Explore Membrane Organization and Transport 楚慧郢,张跃斌,李焱,李国辉 Membrane Biophysics 2017


Multiscale Simulations on Spectral Tuning and the Photoisomerization Mechanism in Fluorescent RNA Spinach 李欣,Chung Lung Wa ,李国辉 Journal of Chemical Theory and Computation 2016


Mediation mechanism of tyrosine 185 on the retinal isomerization equilibrium and the proton release channel in the seven-transmembrane receptor bacteriorhodopsin Ding Xiaoyan, 王洪磊, Peng Bo,Cui Haolin,Gao Yujiao,Iuga Dinu,Judge Peter J, 李国辉,Watts Anthony,Zhao Xin BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016


Wedelolactone enhances osteoblastogenesis by regulating Wnt/beta-catenin signaling pathway but suppresses osteoclastogenesis by NF-kappa B/c-fos/NFATc1 pathway Liu YanQiu,Hong ZhiLai,Zhan LiBin,楚慧郢,Zhang XiaoZhe,李国辉 Scientific Reports 2016


Moderate and strong static magnetic fields directly affect EGFR kinase domain orientation to inhibit cancer cell proliferation Zhang Lei,Wang Jihao,王洪磊,Wang Wenchao,Li Zhiyuan,Liu Juanjuan,Yang Xingxing,Ji Xinmiao,Luo Yan,Hu Chen,Hou Yubin,He Qianqian,Fang Jun,Wang Junfeng,Liu Qingsong,李国辉,Lu Qingyou, Zhang, Xin Oncotarget 2016


Accurate Evaluation of Ion Conductivity of the Gramicidin A Channel Using a Polarizable Force Field without Any Corrections 彭向达, 张跃斌, 楚慧郢, 李焱, 张鼎林, 曹了然, 李国辉 Journal of Chemical Theory and Computation 2016


Hypotaurine evokes a malignant phenotype in glioma through aberrant hypoxic signaling 高鹏, Yang Chunzhang, Nesvick Cody L, Feldman Michael J.,Sizdahkhani Saman, Liu Huailei, 楚慧郢, Yang Fengxu,Tang Ling,Tian Jing,Zhao Shiguang, 李国辉,Heiss John D.,Liu Yang,Zhuang Zhengping, 许国旺 Oncotarget 2016


Free Energy Simulations with the AMOEBA Polarizable Force Field and Metadynamics on GPU Platform 彭向达, 张跃斌, 楚慧郢, 李国辉 JOURNAL OF COMPUTATIONAL CHEMISTRY 2016


Structural basis for activity regulation of MLL family methyltransferases Li Yanjing,Han Jianming, 张跃斌,Cao Fang,Liu Zhijun,Li Shuai,Wu Jian,Hu Chunyi,Wang Yan,Shuai Jin, Chen Juan, 曹了然, Li Dangsheng,Shi Pan,Tian Changlin, Zhang Jian, Dou Yali, 李国辉,Chen Yong,Lei Ming NATURE 2016


Dynamic Regulation of the 7TM Receptor Bacteriorhodopsin Function under Alkaline pH Conditions Ding Xiaoyan,Cui Haolin, 王洪磊, Gao Yujiao,Peng Bo,Watts, Anthony, 李国辉, Zhao Xin BIOPHYSICAL JOURNAL 2016


The Effect of Codon Mismatch on the Protein Translation System 张鼎林, Chen Danfeng, 曹了然, 李国辉,Cheng Hong PLoS One 2016


Coarse-Grained Modeling of Nucleic Acids Using Anisotropic Gay-Berne and Electric Multipole Potentials 李国辉, 沈虎峻, 张鼎林, 李焱, 王洪磊 Journal of Chemical Theory and Computation 2016


Some polarisable force fields for molecular dynamics simulations of lipids, and bilayers 郭委 ,Cheng Liwei, 楚慧郢, 曹了然, 张德鹏,刘佳慧,Xu Peijun,Zheng Xuefang, 李国辉 MOLECULAR SIMULATION 2016
Understanding enzyme reactions using enhanced sampling techniques 曹了然, Cheng Liwei,汤天宝, 刘佳慧, 张德鹏, Xu Peijun, 李国辉 MOLECULAR SIMULATION 2016


Nuclear AURKA acquires kinase-independent transactivating function to enhance breast cancer stem cell phenotype Zheng Feimeng,Yue Caifeng,李国辉,He Bin,Cheng Wei,Wang Xi,Yan Min,Long Zijie,Qiu Wanshou,Yuan Zhongyu, Xu Jie,Liu Bing, Shi Qian,Lam Eric W.-F., Hung Mien-Chie,Liu Quentin Nature Communications 2016
Prevalent Accumulation of Non-Optimal Codons through Somatic Mutations in Human Cancers 吴旭东,李国辉 PLoS One 2016


Validation of polarizable force field parameters for nucleic acids by inter-molecular interactions 曹了然,Ren Hong,苗菁, 郭委, 李焱, 李国辉 Frontiers of Chemical Science and Engineering 2016


Ultrafast Tracking of a Single Live Virion During the Invagination of a Cell Membrane Pan Yangang,Wang Shaowen,Shan Yuping,张鼎林,Gao Jing,Zhang Min,Liu Shuheng,Cai Mingjun,Xu Haijiao,李国辉,Qin Qiwei,Wang Hongda Small 2015


Flubendazole, FDA-approved anthelmintic, targets breast cancer stem-like cells Hou Zhi-Jie,Luo Xi,Zhang Wei,Peng Fei,Cui Bai,Wu Si-Jin,Zheng Fei-Meng,Xu Jie,Xu Ling-Zhi,Long Zi-Jie,Wang Xue-Ting,李国辉,Wan Xian-Yao,Yang Yong-Liang,Liu Quentin Oncotarget 2015


Insights into the molecular recognition of the granuphilin C2A domain with PI(4,5)P2 Wan Chanjuan,Wu Bo,Song Zhenwei,Zhang Jiahai,楚慧郢,Wang Aoli,Liu Qingsong,Shi Yunyu,李国辉,Wang Junfeng CHEMISTRY AND PHYSICS OF LIPIDS 2015


A bimodal MRI and NIR liposome nanoprobe for tumor targeted molecular imaging Wang Huihui,Wu Hao,沈虎峻,Geng Shaote,Wang Beibei,Wang Yanfang,Ma Xiaojun,李国辉,Tan Mingqian Journal of Materials Chemistry B 2015


Computational discovery and experimental verification of tyrosine kinase inhibitor pazopanib for the reversal of memory and cognitive deficits in rat model neurodegeneration Yang Yongliang,李国辉,Zhao Dongyu,Yu Haoyang,Zheng Xiliang,彭向达,Zhang Xiaoe,付婷,Hu Xiaoqing,Niu Mingshan,Ji Xuefei,Zou Libo,Wang Jin Chemical Science 2015


Binding Modes and Interaction Mechanism Between Different Base Pairs and Methylene Blue Trihydrate: A Quantum Mechanics Study Xu Peijun,Wang Jinguang,XuYong,楚慧郢,沈虎峻,Zhang Depeng,Zhao Meixia,LiuJiahui,李国辉 Advances in Experimental Medicine and Biology 2015


Specific dephosphorylation of Janus Kinase 2 by protein tyrosine phosphatases LiJianzhuo,LiuXidong,楚慧郢,FuXueqi,LiTianbao,HuLianghai,XingShu,李国辉,GuJingkai,ZhaoZhizhuangJoe PROTEOMICS 2015


An Anisotropic Coarse-Grained Model Based on Gay-Berne and Electric Multipole Potentials and its Application to Simulate a DMPC Bilayer in an Implicit Solvent Model 沈虎峻, 李焱, Xu Peijun, 李晓芳, 楚慧郢, 张鼎林,李国辉 JOURNAL OF COMPUTATIONAL CHEMISTRY 2015


Mechanistic insight into the functional transition of the enzyme guanylate kinase induced by a single mutation 张跃斌,Niu Huiyan,李焱,楚慧郢,沈虎峻,张鼎林,李国辉 Scientific Reports 2015


Advancement of Polarizable Force Field and Its Use for Molecular Modeling and Design Xu Peijun,Wang Jinguang,Xu Yong,楚慧郢,Liu Jiahui,Zhao Meixia,Zhang Depeng,Mao Yingchen,Li Beibei,Ding Yang,李国辉 Advances in Experimental Medicine and Biology 2015


Folding Mechanisms of Trefoil Knot Proteins Studied by Molecular Dynamics Simulations and Go-model 吴雪,Xu Peijun,Wang Jinguang,Xu Yong,付婷,Zhang Depeng,Zhao Meixia,Liu Jiahui,沈虎峻,Xiu Zhilong,李国辉 Advances in Experimental Medicine and Biology 2015


Theoretical Studies on the Folding Mechanisms for Different DNA G-quadruplexes 吴雪,Xu Peijun,Wang Jinguang,Xu Yong,付婷,Zhao Meixia,Zhang Depeng,Liu Jiahui,沈虎峻,Xiu Zhilong,李国辉 Advances in Experimental Medicine and Biology 2015


Liposomal nanohybrid cerasomes for mitochondria-targeted drug delivery Yanfang Wang,Beibei Wang,Han Liao,Xiaojie Song,Hao Wu,Huihui Wang,沈虎峻,Xiaojun Ma,Mingqian Tan Journal of Materials Chemistry B 2015


The ONIOM Method and Its Applications Chung Lung Wa,Sameera W. M. C.,Ramozzi Romain ,Page Alister J,Hatanaka Miho,Petrova Galina P.,Harris Travis V,李欣,Ke Zhuofeng,Liu Fengyi,Li Hai-Bei,Ding Lina,Morokuma Keiji CHEMICAL REVIEWS 2015


The hydrophobic contacts between the center of the beta I domain and the alpha 1/alpha 7 helices are crucial for the low-affinity state of integrin alpha(4)beta(7) Liu J,付婷,Peng B,Sun H,楚慧郢,李国辉,Chen JF FEBS Journal 2014


Anisotropic Coarse-Grained Model for Proteins Based On Gay-Berne and Electric Multipole Potentials 沈虎峻,李焱, Ren PY, 张鼎林, 李国辉 Journal of Chemical Theory and Computation 2014


A Sub-Element in PRE enhances nuclear export of intronless mRNAs by recruiting the TREX complex via ZC3H18 Chi BK, Wang K, Du YH, Gui B,Chang XY,Wang LT, Fan J,Chen S,吴旭东,李国辉 NUCLEIC ACIDS RESEARCH 2014


Insight into the binding mode and the structural features of the pyrimidine derivatives as human A(2A) adenosine receptor antagonists Zhang LH,Liu TJ,Wang X,Jinan Wang,李国辉,Li Y, 杨凌, Wang YH BIOSYSTEMS 2014


Comparative transcriptional study on the hydrogen evolution of marine microalga Tetraselmis subcordiformis 曹旭鹏,吴旭东,Chaofan Ji,Changhong Yao,Zhaoan Chen,李国辉,薛松. International Journal of Hydrogen Energy 2014


Theoretical Study on the UVR8 Photoreceptor: Sensing Ultraviolet B by Tryptophan and Dissociation of Homodimer 李欣, Lung Wa Chung, Keiji Morokuma, 李国辉 Journal of Chemical Theory and Computation 2014


Bridging the Missing Link Between Structure and Fidelity of the RNA-Dependent RNA Polymerase from Poliovirus Through Free Energy Simulations 沈虎峻, 李国辉 Journal of Chemical Theory and Computation 2014


N-Heterocyclic Carbene Organocatalytic Reductive beta,beta-Coupling Reactions of Nitroalkenes via Radical Intermediates Du Y,Wang YH,李欣,Shao YL,李国辉,Webster RD, Chi YR Organic Letters 2014


Controlled b-protonation and [4+2] cycloaddition of enals and chalcones via N-heterocyclic carbene/acid catalysis: toward substrate independent reaction Zhenqian Fu, 孙慧, Shaojin Chen, Bhoopendra Tiwari, 李国辉,Yonggui Robin Chi Chemical Communications 2013


A Structural-Based Strategy for Recognition of Transcription Factor Binding Sites 徐贝思, Dustin E. Schones, Yongmei Wang, Haojun Liang, 李国辉 PLOS One 2013


A computational analysis of binding modes and conformation changes of MDM2 induced by p53 and inhibitor bindings Chen JZ, Wang JA, Zhu WL, 李国辉 JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN 2013


Disruption of disulfide restriction at integrin knees induces activation and ligand-independent signaling of alpha(4)beta(7) Zhang K, Pan YD, Qi JP, Yue J, Zhang MB, Xu CQ, 李国辉, Chen JF JOURNAL OF CELL SCIENCE 2013
Theoretical Study of N-Heterocyclic Carbenes-Catalyzed Cascade Annulation of Benzodienones and Enals 孙慧,Fang XQ,Chi YR,李国辉 CHIRALITY 2013


Molecular Recognition of Human Angiotensin-Coverting Enzyme I (hACE I) and Different Inhibitors 楚慧郢,Hanyi Min,Mingbo Zhang,沈虎峻,李国辉 Current Topics in Medicinal Chemistry 2013


Investigation Binding Patterns of Human Carboxylesterase I (hCES I) with Broad Substrates by MD Simulations 楚慧郢,Hanyi Min,Mingbo Zhang,沈虎峻,李国辉 Current Topics in Medicinal Chemistry 2013


Theoretical Elucidation of the Origin for Assembly of the DAP12 Dimer with Only One NKG2C in the Lipid Membrane 孙慧, 楚慧郢,付婷, 沈虎峻, 李国辉 Journal of Physical Chemistry B 2013


Theoretical study on the structures and properties of mixtures of urea and choline chloride 孙慧,李焱,吴雪,李国辉 Journal of Molecular Modeling 2013


COMPARING FOLDING MECHANISMS OF DIFFERENT PRION PROTEINS BY Go MODEL 吴雪,付婷,ZHI-LONG XIU,LIU YIN,JIN-GUANG WANG,李国辉 Journal of Theoretical and Computational Chemistry 2013


UNDERSTANDING THE MOLECULAR MECHANISM OF BINDING MODES OF AURORA A INHIBITORS BY LONG TIME SCALE GPU DYNAMICS 付婷,吴雪,ZHILONG XIU,JINGUANG WANG,LIU YIN,李国辉 Journal of Theoretical and Computational Chemistry 2013


Binding Free Energy Estimation for Protein-Ligand Complex Based on MM-PBSwith Various Partial Charge Models 付婷,Zhong Jin,Zhilong Xiu,李国辉 Current Pharmaceutical Design 2013


Variation in One Residue Associated with the Metal Ion- Dependent Adhesion Site Regulates αIIbβ3 IntegrinLigand Binding Affinity Joel Raborn,付婷,吴雪,Zhilong Xiu,李国辉,Bing-Hao Luo PLOS One 2013


Role of Bivalent Cations in Structural Stabilities of New Drug Targets ——Vaccinia-related Kinases (VRK) from Molecular Dynamics Simulations 付婷,Hong Ren,Jiajing Zhang,Pengyu Ren,Istvan Enyedy,李国辉 Current Pharmaceutical Design 2013


Exploring the Proton Conductance and Drug Resistance of BM2 Channel through Molecular Dynamics Simulations and Free Energy Calculations at Different pH Conditions 张玉新,沈虎峻,Mingbo Zhang,李国辉 Journal of Physical Chemistry B 2013


Coarse-grained simulations for organic molecular liquids based on Gay-Berne and electric multipole potentials Peijun Xu,沈虎峻,Lu Yang,丁杨,李贝贝,Ying Shao,Yingchen Mao,李国辉 Journal of Molecular Modeling 2013


QM/MM MD and free energy simulations of the methylation reactions catalyzed by protein arginine methyltransferase PRMT3 Chu YZ,李国辉,Guo Hong Canadian Journal of Chemistry 2013


The Challenge to the Rule of Homology Modeling: Folding Mechanism Study of Protein GA and GB with High Sequence Identity but Different Native Structures 吴雪, Zhong Jin, Zhilong Xiu ,李国辉 Current Pharmaceutical Design 2013


Exploring the Relationship between Sequences, Structures, Dynamical Behaviors and Functions of New Type Protein Drugs: DARPins 吴雪, Yue Shi, Pengyu Ren, Deping Wang , 李国辉 Current Pharmaceutical Design 2013



--------------------------------------以下为早年文章--------------------------------------------

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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