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