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1 Introduction to Structural Bioinformatics&Qin Xu,Hao Dai,Tangzhen Zhao and Dongqing Wei1

Part Ⅰ Advances in Methods for Structural Bioinformatics11

2 JVM：Java Visual Mapping Tool for Next Generation Sequencing Read&Ye Yang and Juan Liu11

3 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 Li19

4 Systematic Methods for Defining Coarse-Grained Maps in Large Biomolecules&Zhiyong Zhang33

5 Quantum Calculation of Protein NMR Chemical Shifts Based on the Automated Fragmentation Method&Tong Zhu,John Z.H.Zhang and Xiao He49

6 Applications of Rare Event Dynamics on the Free Energy Calculations for Membrane Protein Systems&Yukun Wang,Ruoxu Gu,Huaimeng Fan,Jakob Ulmschneider and Dongqing Wei71

Part Ⅱ 3D-Structure Prediction and Folding Mechanism of Biological Macromolecules85

7 Extended Structure of Rat Islet Amyloid Polypeptide in Solution&Lei Wei,Ping Jiang,Malathy Sony Subramanian Manimekalai,Cornelia Hunke,Gerhard Grüber,Konstantin Pervushin and Yuguang Mu85

8 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 Li93

9 Binding Induced Intrinsically Disordered Protein Folding with Molecular Dynamics Simulation&Haifeng Chen111

10 Theoretical Studies on the Folding Mechanisms for Different DNA G-quadruplexes&Xue Wu,Peijun Xu,Jinguang Wang,Yong Xu,Ting Fu,Meixia Zhao,Depeng Zhang,Jiahui Liu,Hujun Shen,Zhilong Xiu and Guohui Li123

11 RNA Folding：Structure Prediction,Folding Kinetics and Ion Electrostatics&Zhijie Tan,Wenbing Zhang,Yazhou Shi and Fenghua Wang143

Part Ⅲ The Interactions Between Biological Macromolecules and Ligands187

12 Binding Modes and Interaction Mechanism Between Different Base Pairs and Methylene Blue Trihydrate：A Quantum Mechanics Study&Peijun Xu,Jinguang Wang,Yong Xu,Huiying Chu,Hujun Shen,Depeng Zhang,Meixia Zhao,Jiahui Liu and Guohui Li187

13 Drug Inhibition and Proton Conduction Mechanisms of the Influenza A M2 Proton Channel&Ruoxu Gu,Limin Angela Liu and Dongqing Wei205

14 Exploring the Ligand-Protein Networks in Traditional Chinese Medicine：Current Databases,Methods and Applications&Mingzhu Zhao and Dongqing Wei227

Part Ⅳ Functional Analysis of Biological Macromolecules261

15 Evolutionary Optimization of Transcription Factor Binding Motif Detection&Zhao Zhang,Ze Wang,Guoqin Mai,Youxi Luo,Miaomiao Zhao and Fengfeng Zhou261

16 Prediction of Serine/Threonine Phosphorylation Sites in Bacteria Proteins&Zhengpeng Li,Ping Wu,Yuanyuan Zhao,Zexian Liu and Wei Zhao275

17 Bioinformatics Tools for Discovery and Functional Analysis of Single Nucleotide Polymorphisms&Li Li and Dongqing Wei287

18 An Application of QM/MM Simulation：The Second Protonation of Cytochrome P450&Peng Lian and Dongqing Wei311

Part Ⅴ Application of Structural Bioinformatics in Drug Design327

19 Recent Progress on Structural Bioinformatics Research of Cytochrome P450 and Its Impact on Drug Discovery&Tao Zhang and Dongqing Wei327

20 Human Cytochrome P450 and Personalized Medicine&Qi Chen and Dongqing Wei341

21 The α7 nAChR Selective Agonists as Drug Candidates for Alzheimer's Disease&Huaimeng Fan,Ruoxu Gu and Dongqing Wei353

22 Bayesian Analysis of Complex Interacting Mutations in HIV Drug Resistance and Cross-Resistance&Ivan Kozyryev and Jing Zhang367