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  • © 2014

Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes

From Bioinformatics to Molecular Quantum Mechanics

Editors:

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  • Comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes

  • Introduces theory and practice of molecular simulations, bioinformatics methods as well as selected applications of molecular quantum mechanics to the study of biological systems

  • Edited and written by leading scientists in the field

Part of the book series: Springer Series in Bio-/Neuroinformatics (SSBN, volume 1)

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USD 169.00
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  • ISBN: 978-3-642-28554-7
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Table of contents (22 chapters)

  1. Front Matter

    Pages 1-12
  2. Coarse-Grained Protein Models in Structure Prediction

    • Maciej Blaszczyk, Dominik Gront, Sebastian Kmiecik, Katarzyna Ziolkowska, Marta Panek, Andrzej Kolinski
    Pages 25-53
  3. Coarse-Grained Modeling of Protein Dynamics

    • Sebastian Kmiecik, Jacek Wabik, Michal Kolinski, Maksim Kouza, Andrzej Kolinski
    Pages 55-79
  4. Modeling Nucleic Acids at the Residue-Level Resolution

    • Filip Leonarski, Joanna Trylska
    Pages 109-149
  5. Optimizations of Protein Force Fields

    • Yoshitake Sakae, Yuko Okamoto
    Pages 195-247
  6. Enhanced Sampling for Biomolecular Simulations

    • Workalemahu Berhanu, Ping Jiang, Ulrich H. E. Hansmann
    Pages 249-267
  7. Computer Modelling of the Lipid Matrix of Biomembranes

    • Marta Pasenkiewicz-Gierula, Michał Markiewicz
    Pages 317-355
  8. Modeling of Membrane Proteins

    • Dorota Latek, Bartosz Trzaskowski, Szymon Niewieczerzał, Przemysław Miszta, Krzysztof Młynarczyk, Aleksander Debinski et al.
    Pages 357-431
  9. All-Atom Monte Carlo Simulations of Protein Folding and Aggregation

    • Anders Irbäck, Sandipan Mohanty
    Pages 433-444
  10. Molecular Dynamics Studies on Amyloidogenic Proteins

    • Sylwia Rodziewicz-Motowidło, Emilia Sikorska, Justyna Iwaszkiewicz
    Pages 445-481
  11. Low-Frequency, Functional, Modes of Proteins: All-Atom and Coarse-Grained Normal Mode Analysis

    • Adrien Nicolaï, Patrice Delarue, Patrick Senet
    Pages 483-524
  12. Bioinformatical Approaches to Unstructured/Disordered Proteins and Their Interactions

    • Bálint Mészáros, Zsuzsanna Dosztányi, Csaba Magyar, István Simon
    Pages 525-556
  13. Theoretical and Computational Aspects of Protein Structural Alignment

    • Paweł Daniluk, Bogdan Lesyng
    Pages 557-598
  14. Simulation of the Protein Folding Process

    • Roterman Irena, L. Konieczny, M. Banach, D. Marchewka, B. Kalinowska, Z. Baster et al.
    Pages 599-638

About this book

Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics.

This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over the world, address the theory and practice of computer simulation techniques in the study of biological phenomena. The chapters are grouped into four thematic sections dealing with the following topics: the methodology of molecular simulations; applications of molecular simulations; bioinformatics methods and use of experimental information in molecular simulations; and selected applications of molecular quantum mechanics. The book includes an introductory chapter written by Harold A. Scheraga, one of the true pioneers in simulation studies of biomacromolecules.

Keywords

  • Bioinformatics methods
  • Coarse-grained models of protein structure
  • Dynamics of nucleic acids
  • Empirical Force Fields
  • Membrane proteins and lipids
  • Molecular Dynamics
  • Molecular Mechanics
  • Molecular Quantum Mechanics
  • Molecular simulations and modeling
  • Monte Carlo Methods
  • Protein structures and dynamics

Reviews

From the book reviews:

“The purpose of the book is to provide an overview of modern methods and techniques for simulating and modeling biological systems. … the book is an excellent introductory text that could be very useful for graduate students who are just starting research projects and need to establish a broader view of simulation methodologies.” (Alexander Tzanov, Computing Reviews, June, 2014)

Editors and Affiliations

  • , Faculty of Chemistry, University of Gdansk, Gdansk, Poland

    Adam Liwo

Bibliographic Information

Buying options

eBook
USD 169.00
Price excludes VAT (USA)
  • ISBN: 978-3-642-28554-7
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Softcover Book
USD 219.99
Price excludes VAT (USA)