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  • © 2015

Molecular Modeling of Proteins

Editors:

  • Includes cutting-edge methods and protocols involving the molecular modeling of proteins
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

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

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Table of contents (20 protocols)

  1. Front Matter

    Pages i-x
  2. Simulation Methods

    1. Front Matter

      Pages 1-1
    2. Molecular Dynamics Simulations

      • Erik Lindahl
      Pages 3-26
    3. Current Status of Protein Force Fields for Molecular Dynamics Simulations

      • Pedro E. M. Lopes, Olgun Guvench, Alexander D. MacKerell Jr.
      Pages 47-71
    4. Lipid Membranes for Membrane Proteins

      • Andreas Kukol
      Pages 73-90
    5. Molecular Dynamics Simulations of Membrane Proteins

      • Philip C. Biggin, Peter J. Bond
      Pages 91-108
    6. Membrane-Associated Proteins and Peptides

      • Marc F. Lensink
      Pages 109-124
    7. Coarse-Grained Force Fields for Molecular Simulations

      • Jonathan Barnoud, Luca Monticelli
      Pages 125-149
    8. Tackling Sampling Challenges in Biomolecular Simulations

      • Alessandro Barducci, Jim Pfaendtner, Massimiliano Bonomi
      Pages 151-171
    9. Calculation of Binding Free Energies

      • 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. The Use of Experimental Structures to Model Protein Dynamics

      • Ataur R. Katebi, Kannan Sankar, Kejue Jia, Robert L. Jernigan
      Pages 213-236
    3. Computing Ensembles of Transitions with Molecular Dynamics Simulations

      • Juan R. Perilla, Thomas B. Woolf
      Pages 237-252
    4. Simulations and Experiments in Protein Folding

      • Giovanni Settanni
      Pages 289-306
  4. Protein Structure Determination

    1. Front Matter

      Pages 307-307
    2. Comparative Modeling of Proteins

      • Gerald H. Lushington
      Pages 309-330
    3. De Novo Membrane Protein Structure Prediction

      • Timothy Nugent
      Pages 331-350
    4. NMR-Based Modeling and Refinement of Protein 3D Structures

      • Wim F. Vranken, Geerten W. Vuister, Alexandre M. J. J. Bonvin
      Pages 351-380

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.

Editors and Affiliations

  • University of Hertfordshire, Hatfield, United Kingdom

    Andreas Kukol

Bibliographic Information

  • Book Title: Molecular Modeling of Proteins

  • Editors: Andreas Kukol

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-1465-4

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2015

  • Hardcover ISBN: 978-1-4939-1464-7Published: 21 October 2014

  • Softcover ISBN: 978-1-4939-5491-9Published: 30 April 2017

  • eBook ISBN: 978-1-4939-1465-4Published: 20 October 2014

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: X, 474

  • Number of Illustrations: 51 b/w illustrations, 53 illustrations in colour

  • Topics: Protein Science, Computer Appl. in Life Sciences, Protein Structure

Buy it now

Buying options

eBook USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book USD 139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Other ways to access