Biomolecular Modelling and Simulations - 1st Edition - ISBN: 9780128000137, 9780128007891

Biomolecular Modelling and Simulations, Volume 96

1st Edition

Serial Volume Editors: Tatyana Karabencheva-Christova
eBook ISBN: 9780128007891
Hardcover ISBN: 9780128000137
Imprint: Academic Press
Published Date: 30th September 2014
Page Count: 330
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Table of Contents

  • Preface
  • Chapter One: The Interplay Between Molecular Modeling and Chemoinformatics to Characterize Protein–Ligand and Protein–Protein Interactions Landscapes for Drug Discovery
    • Abstract
    • 1 Introduction
    • 2 Characterizing PLIs with Fingerprints
    • 3 Visualization of PLIs and PLIFs: The PLIs Space
    • 4 Exploring SPLIRs
    • 5 Target–Ligand Relationships in Chemogenomics Data Sets
    • 6 Protein–Protein Interactions
    • 7 Conclusions
    • Acknowledgments
  • Chapter Two: Computational Study of Putative Residues Involved in DNA Synthesis Fidelity Checking in Thermus aquaticus DNA Polymerase I
    • Abstract
    • 1 Introduction
    • 2 Methods
    • 3 Results and Discussion
    • 4 Conclusions
  • Chapter Three: New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly
    • Abstract
    • 1 Introduction
    • 2 Predicting Protein–Protein Recognition at the Atomistic Level
    • 3 Tackling Protein–Protein Interactions at Coarse-Grained Resolution
    • 4 Predicting Protein Assembly Using Integrative Modeling
    • 5 Conclusions and Perspectives
    • Acknowledgments
  • Chapter Four: Stability of Amyloid Oligomers
    • Abstract
    • 1 Introduction
    • 2 Effect of Force Field on the Preformed Oligomer
    • 3 Role of Mutations
    • 4 Stability of Cylindrin β-Barrel Amyloid Oligomer Models
    • 5 Amyloid Polymorphism
    • 6 Amyloid Aggregation and Cross Seeding
    • 7 Toxicity Mechanism of Amyloid from Molecular Dynamic Simulations
    • 8 Conclusions and Outlook
    • Acknowledgments
  • Chapter Five: Recent Advances in Transferable Coarse-Grained Modeling of Proteins
    • Abstract
    • 1 Introduction
    • 2 CG Models of Protein
    • 3 Hybrid All-atom/Coarse-Grained (AA/CG) Modeling of Proteins
    • 4 Outlook
    • 5 Conclusions
    • Acknowledgment
  • Chapter Six: Studying Allosteric Regulation in Metal Sensor Proteins Using Computational Methods
    • Abstract
    • 1 Introduction
    • 2 Methods
    • 3 Understanding Protein–DNA Interactions
    • 4 Hydrogen-Bonding Pathway
    • 5 Quantifying Metal-Ion Mediated Allostery
    • 6 Mutant Analyses to Understand the HBP
    • 7 Conclusions
    • Acknowledgments
  • Chapter Seven: Insights in the Mechanism of Action and Inhibition of N-Acylethanolamine Acid Amidase by Means of Computational Methods
    • Abstract
    • 1 Introduction
    • 2 General Information and Catalytic Mechanism of Cysteine Ntn-Hydrolases
    • 3 Inhibition of NAAA by β-Lactones
    • 4 Recent Advances in the Field of Active-Site-Directed NAAA Inhibitors
    • Acknowledgment
  • Chapter Eight: CHARMM-GUI PDB Manipulator for Advanced Modeling and Simulations of Proteins Containing Nonstandard Residues
    • Abstract
    • 1 Introduction
    • 2 Ligand FF Generation
    • 3 MTS Reagents
    • 4 Unnatural Amino Acids
    • 5 Perspectives
    • Acknowledgments
  • Chapter Nine: High-Resolution Modeling of Protein Structures Based on Flexible Fitting of Low-Resolution Structural Data
    • Abstract
    • 1 Introduction
    • 2 Methods
    • 3 Results
    • 4 Discussion
    • Acknowledgment
  • Author Index
  • Subject Index

Description

Published continuously since 1944, the Advances in Protein Chemistry and Structural Biology series is the essential resource for protein chemists. Each volume brings forth new information about protocols and analysis of proteins. Each thematically organized volume is guest edited by leading experts in a broad range of protein-related topics.

Key Features

  • Describes advances in biomolecular modelling and simulations
  • Chapters are written by authorities in their field
  • Targeted to a wide audience of researchers, specialists, and students
  • The information provided in the volume is well supported by a number of high quality illustrations, figures, and tables

Readership

The intended audiences for this volume are researchers and specialists in biomolecular modelling and simulations


Details

No. of pages:
330
Language:
English
Copyright:
© Academic Press 2014
Published:
Imprint:
Academic Press
eBook ISBN:
9780128007891
Hardcover ISBN:
9780128000137

About the Serial Volume Editors

Tatyana Karabencheva-Christova Serial Volume Editor

Dr. Tatyana Karabencheva-Christova works at the Department of Applied Sciences, University of Northumbria, UK.

Affiliations and Expertise

Northumbria University, UK