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Molecular Modeling of Proteins

  • Book
  • © 2008

Overview

Editors:
  1. Andreas Kukol
    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Provides step-by-step protocols presented by world renowned experts in the field
  • Contains authoritative reviews of methods applicable to protein modeling
  • Enables readers to apply state-of-the-art methods to their own research
  • Contains links to downloadable software made available by the authors
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 443)

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Table of contents (19 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Methodology

    1. Molecular Dynamics Simulations

      • Erik R. Lindahl
      Pages 3-23

    2. Monte Carlo Simulations

      • David J. Earl, Michael W. Deem
      Pages 25-36

    3. Hybrid Quantum and Classical Methods for Computing Kinetic Isotope Effects of Chemical Reactions in Solutions and in Enzymes

      • Jiali Gao, Dan T. Major, Yao Fan, Yen-lin Lin, Shuhua Ma, Kin-Yiu Wong
      Pages 37-62

    4. Comparison of Protein Force Fields for Molecular Dynamics Simulations

      • Olgun Guvench, Alexander D. MacKerell Jr.
      Pages 63-88

    5. Normal Modes and Essential Dynamics

      • Steven Hayward, Bert L. de Groot
      Pages 89-106

  4. Molecular Modeling of Membrane Proteins

    1. Molecular Dynamics Simulations of Membrane Proteins

      • Philip C. Biggin, Peter J. Bond
      Pages 147-160

    2. Membrane-Associated Proteins and Peptides

      • Marc F. Lensink
      Pages 161-179

    3. Implicit Membrane Models for Membrane Protein Simulation

      • Michael Feig
      Pages 181-196

  5. Protein Structure Determination

    1. Comparative Modeling of Proteins

      • Gerald H. Lushington
      Pages 199-212

    2. Transmembrane Protein Models Based on High-Throughput Molecular Dynamics Simulations with Experimental Constraints

      • Andrew J. Beevers, Andreas Kukol
      Pages 213-227

    3. Nuclear Magnetic Resonance-Based Modeling and Refinement of Protein Three-Dimensional Structures and Their Complexes

      • Gloria Fuentes, Aalt D. J. van Dijk, Alexandre M. J. J. Bonvin
      Pages 229-255

  6. Conformational Change

    1. Conformational Changes in Protein Function

      • Haiguang Liu, Shubhra Ghosh Dastidar, Hongxing Lei, Wei Zhang, Matthew C. Lee, Yong Duan
      Pages 258-275

    2. Protein Folding and Unfolding by All-Atom Molecular Dynamics Simulations

      • Hongxing Lei, Yong Duan
      Pages 277-295

    3. Modeling of Protein Misfolding in Disease

      • Edyta B. MaÉ«olepsza
      Pages 297-330

  7. Applications to Drug Design

    1. Identifying Putative Drug Targets and Potential Drug Leads

      • David S. Wishart
      Pages 333-351

    2. Receptor Flexibility for Large-Scale In Silico Ligand Screens

      • B. Fischer, H. Merlitz, W. Wenzel
      Pages 353-364

    3. Molecular Docking

      • Garrett M. Morris, Marguerita Lim-Wilby
      Pages 365-382
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Keywords

About this book

Molecular modeling has undergone a remarkable transformation in the last 20 years, as biomolecular simulation moves from the realm of specialists to the wider academic community. Molecular Modeling of Proteins provides thorough introductions and a compilation of step-by-step methods applicable to problems faced by non-specialists – especially those new to the software packages used in molecular modeling. Tips on troubleshooting and avoiding common pitfalls are included in this book, along with chapters covering a wide range of subjects ranging from free energy calculation to applications for drug design. Written by an internationally distinguished panel of investigators and outlining the most striking developments in the field, Molecular Modeling of Proteins is an invaluable resource for those in the industry, as well as a cutting-edge reference for students and professionals in the fields of chemistry, biochemistry, biology, biophysics and bioinformatics.

Reviews

From the reviews:

"This book covers many different aspects of protein modeling and is just one volume in an extremely large series … . might be useful as an overview of the various techniques and methods used for the molecular modeling of proteins." (Andrzej Kloczkowski and Robert L. Jernigan, Journal of the American Chemical Society, Vol. 130 (37), 2008)

Bibliographic Information

  • Book Title: Molecular Modeling of Proteins

  • Editors: Andreas Kukol

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-59745-177-2

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Humana Press 2008

  • Hardcover ISBN: 978-1-58829-864-5Published: 19 February 2008

  • Softcover ISBN: 978-1-61737-812-6Published: 19 November 2010

  • eBook ISBN: 978-1-59745-177-2Published: 30 April 2008

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 390

  • Topics: Protein Science, Biochemistry, general, Proteomics, Molecular Medicine, Bioinformatics

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