Molecular Modeling of Proteins / Edition 1

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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 nonspecialists-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, from free energy calculation to applications for drug design. Written by a panel of internationally distinguished 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.

About the Author:
Andreas Kukol, School of Life Sciences, University of Hertfordshire, Hertfordshire, UK

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Editorial Reviews

From the Publisher
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)

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Product Details

  • ISBN-13: 9781617378126
  • Publisher: Springer-Verlag New York, LLC
  • Publication date: 11/19/2010
  • Series: Methods in Molecular Biology Series, #443
  • Edition description: Softcover reprint of hardcover 1st ed. 2008
  • Edition number: 1
  • Pages: 390
  • Product dimensions: 0.83 (w) x 6.14 (h) x 9.21 (d)

Table of Contents


1 Molecular dynamics simulations Erik R. Lindahl

2 Monte Carlo simulations Michael W. Deem, David J. Earl

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 and Kin-Yiu Wong

4 Comparison of forcefields for molecular dynamics simulations Olgun Guvench and Alexander D. MacKerell, Jr.

5 Normal modes and essential dynamics Steven Hayward and Bert L. de Groot

Free energy calculations

6 Calculation of absolute protein-ligand binding constants with the molelcular dynamics free energy perturbation method Hyung-June Woo

7 Free energy calculations applied to membrane proteins Christophe Chipot

Molecular modeling of membrane proteins

8 Molecular dynamics simulations of membrane proteins Philip C. Biggin and Peter J. Bond

9 Membrane associated proteins and peptides Mark F. Lensink

10 Implicit membrane models for membrane protein simulation Michael Feig

Protein structure determination

11 Comparative Modeling of Proteins Gerald H. Lushington

12 Transmembrane protein models based on high throughput MD simulations with experimental constraints Andrew J. Beevers, Andreas Kukol

13 NMR-based modelling and refinement of protein 3D structures and their complexes G Fuentes, A.D.J. van Dijk and Alexandre M.J.J. Bonvin

Conformational change

14 Conformational changes in protein function Haiguang Liu, Shubhra Ghosh Dastidar, Hongxing Lei, Wei Zhang, Matthew C. Lee, and Yong Duan

15 Protein folding and unfolding by all-atom molecular dynamics simulations Hongxing Lei and Yong Duan

16 Modeling of protein misfolding in disease Edyta B. Malolepsza

Applications to drug design

17 Identifying Putative Drug Targets and Potential Drug Leads: Starting Points for Virtual Screening and Docking David S. Wishart

18 Receptor flexibility for large scale in-silico ligand screens: chances and challenges B. Fisher, H. Merlitz and Wolfgang Wenzel

19 Molecular docking Garrett M. Morris and Marguerita Lim-Wilby

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