1 Introduction to Structural Bioinformatics Qin Xu, Hao Dai, Tangzhen Zhao and Dongqing Wei Part I Advances in Methods for Structural Bioinformatics2 JVM: Java Visual Mapping Tool for Next Generation Sequencing Read Ye Yang and Juan Liu3 Advancement of Polarizable Force Field and Its Use for Molecular Modeling and Design Peijun Xu, Jinguang Wang, Yong Xu, Huiying Chu, Jiahui Liu, Meixia Zhao, Depeng Zhang, Yingchen Mao, Beibei Li, Yang Ding and Guohui Li4 Systematic Methods for Defining Coarse-Grained Maps in Large Biomolecules Zhiyong Zhang5 Quantum Calculation of Protein NMR Chemical Shifts Basedon the Automated Fragmentation Method Tong Zhu, John Z.H. Zhang and Xiao He6 Applications of Rare Event Dynamics on the Free Energy Calculations for Membrane Protein Systems Yukun Wang, Ruoxu Gu, Huaimeng Fan,Jakob Ulmschneider and Dongqing Wei Part II 3D-Structure Prediction and Folding Mechanism of Biological Macromolecules7 Extended Structure of Rat Islet Amyloid Polypeptide in Solution Lei Wei, Ping Jiang, Malathy Sony Subramanian Manimekalai, Cornelia Hunke, Gerhard Grtiber, Konstantin Pervushin and Yuguang Mu8 Folding Mechanisms of Trefoil Knot Proteins Studied by Molecular Dynamics Simulations and Go-model Xue Wu, Peijun Xu, Jinguang Wang, Yong Xu, Ting Fu, Depeng Zhang, Meixia Zhao, Jiahui Liu, Hujun Shen, Zhilong Xiu and Guohui Li9 Binding Induced Intrinsically Disordered Protein Folding with Molecular Dynamics Simulation Haifeng Chen10 Theoretical Studies on the Folding Mechanisms for DifferentDNA G-quadruplexes Xue Wu, Peijun Xu, Jinguang Wang, Yong Xu, Ting Fu, Meixia Zhao, Depeng Zhang, Jiahui Liu, Hu]un Shen,Zhilong Xiu and Guohui Li11 RNA Folding: Structure Prediction, Folding Kinetics and Ion Electrostatics Zhijie Tan, Wenbing Zhang, Yazhou Shi and Fenghua WangPart III The Interactions Between Biological Macromoleculesand Ligands12 Binding Modes and Interaction Mechanism Between DifferentBase Pairs and Methylene Blue Trihydrate:A Quantum Mechanics StudyPeijun Xu, Jinguang Wang, Yong Xu, Huiying Chu, Hujun Shen,Depeng Zhang, Meixia Zhao, Jiahui Liu and Guohui Li13 Drug Inhibition and Proton Conduction Mechanismsof the Influenza A M2 Proton ChannelRuoxu Gu, Limin Angela Liu and Dongqing Wei14 Exploring the Ligand-Protein Networks in TraditionalChinese Medicine: Current Databases, Methods and ApplicationsMingzhu Zhao and Dongqing WeiPart IV Functional Analysis of Biological Macromolecules15 Evolutionary Optimization of Transcription FactorBinding Motif DetectionZhao Zhang, Ze Wang, Guoqin Mai, Youxi Luo,Miaomiao Zhao and Fengfeng Zhou16 Prediction of Serine/Threonine Phosphorylation Sitesin Bacteria ProteinsZhengpeng Li, Ping Wu, Yuanyuan Zhao,Zexian Liu and Wei Zhao17 Bioinformatics Tools for Discovery and Functional Analysisof Single Nucleotide PolymorphismsLi Li and Dongqing Wei18 An Application of QM/MM Simulation: The Second Protonation of Cytochrome P450 Peng Lian and Dongqing Wei Part V Application of Structural Bioinformatics in Drug Design19 Recent Progress on Structural Bioinformatics Research of Cytochrome P450 and Its Impact on Drug Discovery Tao Zhang and Dongqing Wei20 Human Cytochrome P450 and Personalized Medicine Qi Chen and Dongqing Wei21 The α7 nAChR Selective Agonists as Drug Candidates for Alzheimer's Disease Huaimeng Fan, Ruoxu Gu and Dongqing Wei22 Bayesian Analysis of Complex Interacting Mutationsin HIV Drug Resistance and Cross-Resistance Ivan Kozyryev and Jing Zhang
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