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