Molecular Modeling of Proteins

  • Andreas Kukol

Part of the Methods in Molecular Biology book series (MIMB, volume 1215)

Table of contents

  1. Front Matter
    Pages i-x
  2. Simulation Methods

    1. Front Matter
      Pages 1-1
    2. Erik Lindahl
      Pages 3-26
    3. Pedro E. M. Lopes, Olgun Guvench, Alexander D. MacKerell Jr.
      Pages 47-71
    4. Andreas Kukol
      Pages 73-90
    5. Philip C. Biggin, Peter J. Bond
      Pages 91-108
    6. Marc F. Lensink
      Pages 109-124
    7. Jonathan Barnoud, Luca Monticelli
      Pages 125-149
    8. Alessandro Barducci, Jim Pfaendtner, Massimiliano Bonomi
      Pages 151-171
    9. Vytautas Gapsys, Servaas Michielssens, Jan Henning Peters, Bert L. de Groot, Hadas Leonov
      Pages 173-209
  3. Conformational Change

    1. Front Matter
      Pages 211-211
    2. Ataur R. Katebi, Kannan Sankar, Kejue Jia, Robert L. Jernigan
      Pages 213-236
    3. Juan R. Perilla, Thomas B. Woolf
      Pages 237-252
    4. Giovanni Settanni
      Pages 289-306
  4. Protein Structure Determination

    1. Front Matter
      Pages 307-307
    2. Gerald H. Lushington
      Pages 309-330
    3. Timothy Nugent
      Pages 331-350
    4. Wim F. Vranken, Geerten W. Vuister, Alexandre M. J. J. Bonvin
      Pages 351-380
  5. Protein–Ligand Interactions

    1. Front Matter
      Pages 381-381
    2. Zhong-Ru Xie, Ming-Jing Hwang
      Pages 383-398
    3. João P. G. L. M. Rodrigues, Ezgi Karaca, Alexandre M. J. J. Bonvin
      Pages 399-424
    4. Jesper Sørensen, Özlem Demir, Robert V. Swift, Victoria A. Feher, Rommie E. Amaro
      Pages 445-469
  6. Back Matter
    Pages 471-474

About this book


Molecular Modeling of Proteins, Second Edition provides a theoretical background of various methods available and enables non-specialists to apply methods to their problems by including updated chapters and new material not covered in the first edition. This detailed volume opens by featuring classical and advanced simulation methods as well as methods to set-up complex systems such as lipid membranes and membrane proteins, and continues with chapters devoted to the simulation and analysis of conformational changes of proteins, computational methods for protein structure prediction, usage of experimental data in combination with computational techniques, as well as protein-ligand interactions, which are relevant in the drug design process. Written for the highly successful Methods in Molecular Biology series, chapters include thorough introductions, step-by-step instructions, and notes on troubleshooting and avoiding common pitfalls.

Update-to-date and authoritative, Molecular Modeling of Proteins, Second Edition aims to aid researchers in the physical, chemical, and biosciences interested in utilizing this powerful technology.


Biomolecule simulation Computational methods Membrane proteins Molecular modeling Protein structure prediction Simulation methods

Editors and affiliations

  • Andreas Kukol
    • 1
  1. 1.University of HertfordshireHatfieldUnited Kingdom

Bibliographic information

  • DOI
  • Copyright Information Springer Science+Business Media New York 2015
  • Publisher Name Humana Press, New York, NY
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-4939-1464-7
  • Online ISBN 978-1-4939-1465-4
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site