Molecular Modeling of Proteins / Edition 1

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Overview

Molecular modeling has undergone a remarkable transformation in the last 20 years. This book 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 the book, along with chapters covering a wide range of subjects. Links to downloadable software are also provided.

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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

Methodology 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 IdentifyingPutative 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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