Authors:
- Computer simulations have become a standard tool for exploring biomolecules, often in conjunction with experimentally derived data
- Introductory self-contained course by which students with a relatively limited background in chemistry, biology and computer literacy, can learn the fundamentals of biomolecular simulations
- The material on which the Hands-On Guide is based was developed and tested at Harvard University during the last 15 years
- Integrated exercises that involve the use of one of the premiere molecular dynamics programs CHARMM and the widely used graphics program CHARMM
- The fact that the programs used are widely distributed and generally available makes an introduction to them of importance for the future research career of students
- Includes supplementary material: sn.pub/extras
Part of the book series: Focus on Structural Biology (FOSB, volume 4)
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Table of contents (17 chapters)
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Front Matter
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Back Matter
About this book
Molecular dynamics simulations have become instrumental in replacing our view of proteins as relatively rigid structures with the realization that they were dynamic systems, whose internal motions play a functional role. Over the years, such simulations have become a central part of biophysics. Applications of molecular dynamics in biophysics range over many areas. They are used in the structure determination of macromolecules with x-ray and NMR data, the modelling of unknown structures from their sequence, the study of enzyme mechanisms, the estimation of ligand-binding free energies, the evaluation of the role of conformational change in protein function, and drug design for targets of known structures.
The widespread application of molecular dynamics and related methodologies suggests that it would be useful to have available an introductory self-contained course by which students with a relatively limited background in chemistry, biology and computer literacy, can learn the fundamentals of the field. This Guide to Biomolecular Simulations tries to fill this need. The Guide consists of six chapters which provide the fundamentals of the field and six chapters which introduce the reader to more specialized but important applications of the methodology.
Reviews
From the reviews:
"The Guide to Biomolecular Simulations intends to provide students and nonexperts with an introductory, self-contained course about the application of molecular dynamics and related methodologies. The book emerged from a biophysics course held at Harvard in the 1990s and is therefore suited for standalone self-study as well as for classroom use … . And finally, a reader who successfully worked through the book obtained significant experience in using CHARMM, one of the most widely used molecular dynamics packages in biomolecular simulations." (Anselm H. C. Horn, Journal of Chemical Information and Modeling, Vol. 46 (6), 2006)
Authors and Affiliations
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Predix Pharmaceuticals, Ramat-Gan, Israel
Oren M. Becker
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Harvard University, Cambridge, USA
Martin Karplus
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Université Louis Pasteur, Strasbourg, France
Martin Karplus
Bibliographic Information
Book Title: Guide to Biomolecular Simulations
Authors: Oren M. Becker, Martin Karplus
Series Title: Focus on Structural Biology
DOI: https://doi.org/10.1007/1-4020-3587-X
Publisher: Springer Dordrecht
eBook Packages: Chemistry and Materials Science, Chemistry and Material Science (R0)
Copyright Information: Springer Science+Business Media B.V. 2006
Softcover ISBN: 978-94-017-7635-6Published: 23 August 2016
eBook ISBN: 978-1-4020-3587-6Published: 26 June 2006
Series ISSN: 1571-4853
Series E-ISSN: 2542-9566
Edition Number: 1
Number of Pages: IX, 203
Topics: Computer Applications in Chemistry, Computer Appl. in Life Sciences, Biological and Medical Physics, Biophysics, Theoretical and Computational Chemistry