Advance in Structural Bioinformatics

Editors:

ISBN: 978-94-017-9244-8 (Print) 978-94-017-9245-5 (Online)

Table of contents (22 chapters)

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  1. Front Matter

    Pages i-xi

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    Chapter

    Pages 1-7

    Introduction to Structural Bioinformatics

  3. Advances in Methods for Structural Bioinformatics

    1. Front Matter

      Pages 9-9

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      Chapter

      Pages 11-18

      JVM: Java Visual Mapping Tool for Next Generation Sequencing Read

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      Chapter

      Pages 19-32

      Advancement of Polarizable Force Field and Its Use for Molecular Modeling and Design

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      Chapter

      Pages 33-48

      Systematic Methods for Defining Coarse-Grained Maps in Large Biomolecules

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      Chapter

      Pages 49-70

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

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      Chapter

      Pages 71-82

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

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

    1. Front Matter

      Pages 83-83

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      Chapter

      Pages 85-92

      Extended Structure of Rat Islet Amyloid Polypeptide in Solution

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      Chapter

      Pages 93-110

      Folding Mechanisms of Trefoil Knot Proteins Studied by Molecular Dynamics Simulations and Go-model

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      Chapter

      Pages 111-121

      Binding Induced Intrinsically Disordered Protein Folding with Molecular Dynamics Simulation

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      Chapter

      Pages 123-141

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

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      Chapter

      Pages 143-183

      RNA Folding: Structure Prediction, Folding Kinetics and Ion Electrostatics

  5. The Interactions Between Biological Macromolecules and Ligands

    1. Front Matter

      Pages 185-185

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      Chapter

      Pages 187-203

      Binding Modes and Interaction Mechanism Between Different Base Pairs and Methylene Blue Trihydrate: A Quantum Mechanics Study

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      Chapter

      Pages 205-226

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

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      Chapter

      Pages 227-257

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

  6. Functional Analysis of Biological Macromolecules

    1. Front Matter

      Pages 259-259

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      Chapter

      Pages 261-274

      Evolutionary Optimization of Transcription Factor Binding Motif Detection

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      Chapter

      Pages 275-285

      Prediction of Serine/Threonine Phosphorylation Sites in Bacteria Proteins

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      Chapter

      Pages 287-310

      Bioinformatics Tools for Discovery and Functional Analysis of Single Nucleotide Polymorphisms

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      Chapter

      Pages 311-324

      An Application of QM/MM Simulation: The Second Protonation of Cytochrome P450

  7. Application of Structural Bioinformatics in Drug Design

    1. Front Matter

      Pages 325-325

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      Chapter

      Pages 327-339

      Recent Progress on Structural Bioinformatics Research of Cytochrome P450 and Its Impact on Drug Discovery

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      Chapter

      Pages 341-351

      Human Cytochrome P450 and Personalized Medicine

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