Advance in Structural Bioinformatics

1. Front Matter

   Pages i-xi

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2. Introduction to Structural Bioinformatics

   • Qin Xu, Hao Dai, Tangzhen Zhao, Dongqing Wei

   Pages 1-7

3. Advances in Methods for Structural Bioinformatics

   1. Front Matter

      Pages 9-9

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   2. JVM: Java Visual Mapping Tool for Next Generation Sequencing Read

      • Ye Yang, Juan Liu

      Pages 11-18

   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 et al.

      Pages 19-32

   4. Systematic Methods for Defining Coarse-Grained Maps in Large Biomolecules

      • Zhiyong Zhang

      Pages 33-48

   5. Quantum Calculation of Protein NMR Chemical Shifts Based on the Automated Fragmentation Method

      • Tong Zhu, John Z. H. Zhang, Xiao He

      Pages 49-70

   6. Applications of Rare Event Dynamics on the Free Energy Calculations for Membrane Protein Systems

      • Yukun Wang, Ruoxu Gu, Huaimeng Fan, Jakob Ulmschneider, Dongqing Wei

      Pages 71-82

4. 3D-Structure Prediction and Folding Mechanism of Biological Macromolecules

   1. Front Matter

      Pages 83-83

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   2. Extended Structure of Rat Islet Amyloid Polypeptide in Solution

      • Lei Wei, Ping Jiang, Malathy Sony Subramanian Manimekalai, Cornelia Hunke, Gerhard Grüber, Konstantin Pervushin et al.

      Pages 85-92

   3. 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 et al.

      Pages 93-110

   4. Binding Induced Intrinsically Disordered Protein Folding with Molecular Dynamics Simulation

      • Haifeng Chen

      Pages 111-121

   5. Theoretical Studies on the Folding Mechanisms for Different DNA G-quadruplexes

      • Xue Wu, Peijun Xu, Jinguang Wang, Yong Xu, Ting Fu, Meixia Zhao et al.

      Pages 123-141

   6. RNA Folding: Structure Prediction, Folding Kinetics and Ion Electrostatics

      • Zhijie Tan, Wenbing Zhang, Yazhou Shi, Fenghua Wang

      Pages 143-183

5. The Interactions Between Biological Macromolecules and Ligands

   1. Front Matter

      Pages 185-185

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   2. 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 et al.

      Pages 187-203

   3. Drug Inhibition and Proton Conduction Mechanisms of the Influenza A M2 Proton Channel

      • Ruoxu Gu, Limin Angela Liu, Dongqing Wei

      Pages 205-226

   4. Exploring the Ligand-Protein Networks in Traditional Chinese Medicine: Current Databases, Methods and Applications

      • Mingzhu Zhao, Dongqing Wei

      Pages 227-257

6. Functional Analysis of Biological Macromolecules

   1. Front Matter

      Pages 259-259

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   2. Evolutionary Optimization of Transcription Factor Binding Motif Detection

      • Zhao Zhang, Ze Wang, Guoqin Mai, Youxi Luo, Miaomiao Zhao, Fengfeng Zhou

      Pages 261-274

This text examines in detail mathematical and physical modeling, computational methods and systems for obtaining and analyzing biological structures, using pioneering research cases as examples. As such, it emphasizes programming and problem-solving skills. It provides information on structure bioinformatics at various levels, with individual chapters covering introductory to advanced aspects, from fundamental methods and guidelines on acquiring and analyzing genomics and proteomics sequences, the structures of protein, DNA and RNA, to the basics of physical simulations and methods for conformation searches. This book will be of immense value to researchers and students in the fields of bioinformatics, computational biology and chemistry. Dr. Dongqing Wei is a Professor at the Department of Bioinformatics and Biostatistics, College of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai, China. His research interest is in the general area of structural bioinformatics.

• Biological Macromolecules
• Molecular Modeling
• Structural Predictions
• Structural bioinformatics

• Shanghai JiaoTong University, Shanghai, China

  Dongqing Wei

• Shanghai Jiao Tong University, Shanghai, China

  Qin Xu, Tangzhen Zhao, Hao Dai

Dr. Dongqing Wei is professor at the Department of Bioinformatics and Biostatistics, College of Life Science and Biotechnology, Shanghai Jiaotong University, China. He serves as Editor-in-Chief for journal of Interdisciplinary Sciences-Computational Life Sciences. He is chairman of International Association of Scientists in the Interdisciplinary Areas (IASIA). Prof. Wei’s research is in the general area of structural bioinformatics. He has made many important contributions to sciences. With more than 150 journal papers and SCI 3000 citations, he is becoming a leading figure in the area of structural bioinformatics. Prof. Wei organized a few important international conferences recently, for example, International Conference on Computational and System Biology, 2009-2011, Shanghai, China; Theory and Application of Computational Chemistry, Sept. 23-27, 2008, Shanghai, China; 2nd IEEE Conferences on Bioinformatics and Biomedical Engineering, May 16-20, 2008, Shanghai, China.

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