1 Introduction to Structural Bioinformatics&Qin Xu,Hao Dai,Tangzhen Zhao and Dongqing Wei 1
Part Ⅰ Advances in Methods for Structural Bioinformatics 11
2 JVM：Java Visual Mapping Tool for Next Generation Sequencing Read&Ye Yang and Juan Liu 11
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 Li 19
4 Systematic Methods for Defining Coarse-Grained Maps in Large Biomolecules&Zhiyong Zhang 33
5 Quantum Calculation of Protein NMR Chemical Shifts Based on the Automated Fragmentation Method&Tong Zhu,John Z.H.Zhang and Xiao He 49
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 Wei 71
Part Ⅱ 3D-Structure Prediction and Folding Mechanism of Biological Macromolecules 85
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 Mu 85
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 Li 93
9 Binding Induced Intrinsically Disordered Protein Folding with Molecular Dynamics Simulation&Haifeng Chen 111
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 Li 123
11 RNA Folding：Structure Prediction,Folding Kinetics and Ion Electrostatics&Zhijie Tan,Wenbing Zhang,Yazhou Shi and Fenghua Wang 143
Part Ⅲ The Interactions Between Biological Macromolecules and Ligands 187
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 Li 187
13 Drug Inhibition and Proton Conduction Mechanisms of the Influenza A M2 Proton Channel&Ruoxu Gu,Limin Angela Liu and Dongqing Wei 205
14 Exploring the Ligand-Protein Networks in Traditional Chinese Medicine：Current Databases,Methods and Applications&Mingzhu Zhao and Dongqing Wei 227
Part Ⅳ Functional Analysis of Biological Macromolecules 261
15 Evolutionary Optimization of Transcription Factor Binding Motif Detection&Zhao Zhang,Ze Wang,Guoqin Mai,Youxi Luo,Miaomiao Zhao and Fengfeng Zhou 261
16 Prediction of Serine/Threonine Phosphorylation Sites in Bacteria Proteins&Zhengpeng Li,Ping Wu,Yuanyuan Zhao,Zexian Liu and Wei Zhao 275
17 Bioinformatics Tools for Discovery and Functional Analysis of Single Nucleotide Polymorphisms&Li Li and Dongqing Wei 287
18 An Application of QM/MM Simulation：The Second Protonation of Cytochrome P450&Peng Lian and Dongqing Wei 311
Part Ⅴ Application of Structural Bioinformatics in Drug Design 327
19 Recent Progress on Structural Bioinformatics Research of Cytochrome P450 and Its Impact on Drug Discovery&Tao Zhang and Dongqing Wei 327
20 Human Cytochrome P450 and Personalized Medicine&Qi Chen and Dongqing Wei 341
21 The α7 nAChR Selective Agonists as Drug Candidates for Alzheimer's Disease&Huaimeng Fan,Ruoxu Gu and Dongqing Wei 353
22 Bayesian Analysis of Complex Interacting Mutations in HIV Drug Resistance and Cross-Resistance&Ivan Kozyryev and Jing Zhang 367