Skip to main content
SpringerLink
Log in

Advance in Structural Bioinformatics

  • Book
  • © 2015

Overview

Editors:
  1. Dongqing Wei

    1. Shanghai JiaoTong University, Shanghai, China

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  2. Qin Xu

    1. Shanghai Jiao Tong University, Shanghai, China

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  3. Tangzhen Zhao

    1. Shanghai Jiao Tong University, Shanghai, China

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  4. Hao Dai

    1. Shanghai Jiao Tong University, Shanghai, China

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Presents the core algorithms and mathematical models for sequence analysis
  • Provides systematic and detailed methodologies and application
  • Includes the most recent progress in the field
  • Includes supplementary material: sn.pub/extras

Part of the book series: Advances in Experimental Medicine and Biology (AEMB, volume 827)

This is a preview of subscription content, log in via an institution to check access.

Access this book

Log in via an institution
eBook USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Other ways to access

Licence this eBook for your library

Institutional subscriptions

Table of contents (22 chapters)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  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
      Download chapter PDF

    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
      Download chapter PDF

    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
      Download chapter PDF

    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
      Download chapter PDF

    2. Evolutionary Optimization of Transcription Factor Binding Motif Detection

      • Zhao Zhang, Ze Wang, Guoqin Mai, Youxi Luo, Miaomiao Zhao, Fengfeng Zhou
      Pages 261-274
Back to top

Keywords

About this book

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.

Editors and Affiliations

  • Shanghai JiaoTong University, Shanghai, China

    Dongqing Wei

  • Shanghai Jiao Tong University, Shanghai, China

    Qin Xu, Tangzhen Zhao, Hao Dai

About the editors

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.

Bibliographic Information

Publish with us

Policies and ethics

Back to top

Search

Navigation