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

From Bioinformatics to Molecular Quantum Mechanics

  • Adam Liwo

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

Table of contents

  1. Front Matter
    Pages 1-12
  2. Maciej Blaszczyk, Dominik Gront, Sebastian Kmiecik, Katarzyna Ziolkowska, Marta Panek, Andrzej Kolinski
    Pages 25-53
  3. Sebastian Kmiecik, Jacek Wabik, Michal Kolinski, Maksim Kouza, Andrzej Kolinski
    Pages 55-79
  4. Filip Leonarski, Joanna Trylska
    Pages 109-149
  5. Yoshitake Sakae, Yuko Okamoto
    Pages 195-247
  6. Workalemahu Berhanu, Ping Jiang, Ulrich H. E. Hansmann
    Pages 249-267
  7. Marta Pasenkiewicz-Gierula, Michał Markiewicz
    Pages 317-355
  8. Dorota Latek, Bartosz Trzaskowski, Szymon Niewieczerzał, Przemysław Miszta, Krzysztof Młynarczyk, Aleksander Debinski et al.
    Pages 357-431
  9. Anders Irbäck, Sandipan Mohanty
    Pages 433-444
  10. Sylwia Rodziewicz-Motowidło, Emilia Sikorska, Justyna Iwaszkiewicz
    Pages 445-481
  11. Adrien Nicolaï, Patrice Delarue, Patrick Senet
    Pages 483-524
  12. Bálint Mészáros, Zsuzsanna Dosztányi, Csaba Magyar, István Simon
    Pages 525-556
  13. Paweł Daniluk, Bogdan Lesyng
    Pages 557-598
  14. Roterman Irena, L. Konieczny, M. Banach, D. Marchewka, B. Kalinowska, Z. Baster et al.
    Pages 599-638

About this book

Introduction

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

Editors and affiliations

  • Adam Liwo
    • 1
  1. 1., Faculty of ChemistryUniversity of GdanskGdanskPoland

Bibliographic information

  • DOI https://doi.org/10.1007/978-3-642-28554-7
  • Copyright Information Springer-Verlag Berlin Heidelberg 2014
  • Publisher Name Springer, Berlin, Heidelberg
  • eBook Packages Engineering
  • Print ISBN 978-3-642-28553-0
  • Online ISBN 978-3-642-28554-7
  • Series Print ISSN 2193-9349
  • Series Online ISSN 2193-9357
  • About this book