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 on Bio- and Neurosystems book series (SSBN, volume 8)

Table of contents

  1. Front Matter
    Pages i-xv
  2. Introduction

    1. Front Matter
      Pages 1-1
  3. Molecular Simulations: Methodology

    1. Front Matter
      Pages 25-25
    2. Maciej Blaszczyk, Dominik Gront, Sebastian Kmiecik, Mateusz Kurcinski, Michal Kolinski, Maciej Pawel Ciemny et al.
      Pages 27-59
    3. Sebastian Kmiecik, Jacek Wabik, Michal Kolinski, Maksim Kouza, Andrzej Kolinski
      Pages 61-87
    4. Filip Leonarski, Joanna Trylska
      Pages 117-161
    5. Yoshitake Sakae, Yuko Okamoto
      Pages 203-256
    6. Workalemahu Berhanu, Ping Jiang, Ulrich H. E. Hansmann
      Pages 257-280
  4. Molecular Simulations: Applications

    1. Front Matter
      Pages 305-305
    2. Marta Pasenkiewicz-Gierula, Michał Markiewicz
      Pages 331-370
    3. Dorota Latek, Bartosz Trzaskowski, Szymon Niewieczerzał, Przemysław Miszta, Krzysztof Młynarczyk, Aleksander Dębiński et al.
      Pages 371-451
    4. Daniel Nilsson, Sandipan Mohanty, Anders Irbäck
      Pages 453-466
    5. Sylwia Rodziewicz-Motowidło, Emilia Sikorska, Justyna Iwaszkiewicz
      Pages 467-499
    6. Maksim Kouza, Andrzej Kolinski, Irina Alexandra Buhimschi, Andrzej Kloczkowski
      Pages 541-558
  5. Use of Structural Database or Experimental Information in Modeling Protein Structure and Dynamics

    1. Front Matter
      Pages 559-559
    2. Bálint Mészáros, Zsuzsanna Dosztányi, Erzsébet Fichó, Csaba Magyar, István Simon
      Pages 561-596
    3. Paweł Daniluk, Bogdan Lesyng
      Pages 597-637
    4. M. Banach, L. Konieczny, I. Roterman
      Pages 639-658
  6. Applications of Molecular Quantum Mechanics

  7. Back Matter
    Pages 851-851

About this book


This book provides a comprehensive overview of modern computer-based techniques for analyzing the structure, properties and dynamics of biomolecules and biomolecular processes. It is organized in four main parts; the first one deals with methodology of molecular simulations; the second one with applications of molecular simulations; the third one introduces bioinformatics methods and the use of experimental information in molecular simulations; the last part reports on selected applications of molecular quantum mechanics. This second edition has been thoroughly revised and updated to include the latest progresses made in the respective field of research.


Bioinformatics methods Amyloid formation and stability Coarse-grained models of protein structure Coarse-grained models of nucleic acids Dynamics of nucleic acids Empirical force fields Membrane proteins and lipids Metaloenzymes Molecular dynamics Molecular mechanics Molecular quantum mechanics Molecular simulations and modeling Monte Carlo methods Protein structure prediction Protein dynamics

Editors and affiliations

  • Adam Liwo
    • 1
  1. 1.Faculty of ChemistryUniversity of GdańskGdańskPoland

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