Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems, 1st Edition (Hardback) book cover

Normal Mode Analysis

Theory and Applications to Biological and Chemical Systems, 1st Edition

Edited by Qiang Cui, Ivet Bahar

Chapman and Hall/CRC

432 pages | 32 Color Illus. | 124 B/W Illus.

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pub: 2005-12-12
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Rapid developments in experimental techniques continue to push back the limits in the resolution, size, and complexity of the chemical and biological systems that can be investigated. This challenges the theoretical community to develop innovative methods for better interpreting experimental results. Normal Mode Analysis (NMA) is one such technique. Capable of providing unique insights into the structural and dynamical properties of complex systems, it is now finding a wide range of applications in chemical and biological problems.

From the fundamental physical ideas to cutting-edge applications and beyond, this book presents a broad overview of normal mode analysis and its value in state-of-the-art research. The first section introduces NMA, examines NMA algorithm development at different resolutions, and explores the application of those techniques in the study of biological systems. Later chapters cover method developments based on or inspired by NMA but going beyond the harmonic approximation inherent in standard NMA techniques.

Normal mode analysis complements traditional approaches with computational efficiency and applicability to large systems that are beyond the reach of older methods. This book offers a unique opportunity to learn from the experiences of an international, interdisciplinary panel of top researchers and explore the latest developments and applications of NMA to biophysical and chemical problems.

Table of Contents

Normal mode theory and harmonic potential approximations

Konrad Hinsen

All-atom normal mode calculations of large molecular systems using iterative methods

Liliane Mouawad and David Perahia

The Gaussian network model: Theory and applications

A.J. Radar, Chakra Chennubhotla, Lee-Wei Yang, Ivet Bahar

Normal mode analysis of macromolecules: from enzyme activity site to molecular machines

Guohui Li, Adam Van Wynsbergh, Omar N.A. Demerdash, Qiang Cui

Functional information from slow mode shapes

Yves-Henri Sanejouand

Unveiling molecular mechanisms of biological functions in large macromolecular assemblies using elastic network normal mode analysis

Florence Tama, Charles L. Brooks III

Applications of normal mode analysis in structural refinement of supramolecular complexes

Jianpeng Ma

Normal mode analysis in studying protein motions with x-ray crystallography

George N. Phillips, Jr.

Optimizing the parameters of the Gaussian network model for ATP-binding proteins

Taner Z. Sen, Robert L. Jernigan

Effects of sequence, cyclization, and superhelical stress on the internet motions of DNA

Atsushi Matsumoto, Wilma K. Olson

Symmetry in normal mode analysis of icosahedral viruses

Herman W.T. van Vlijmen

Extension of the normal mode concept: Principal component analysis, jumping-among-minima model, and their applications to experimental data analysis

Akio Kitao

Imaginary-frequency, unstable instantaneous normal modes, the potential energy landscape, and diffusion in liquids


Driven molecular dynamics for normal modes of biomolecules without the Hessian, and beyond

Martina Kaledin, Alexey L. Kaledin, Alex Brown, and Joel Bowman

Probing vibrational energy relaxation in proteins using normal modes

Hiroshi Fujisaki, Lintao Bu, and John E. Straub

Anharmonic decay of vibrational state in proteins

Xin Yu, David M. Leitner

Collective coordinate approaches to extended conformational sampling

Michael Nilges, Rogher Abseher

Using collective coordinates to guide conformational sampling in atomic simulations

Haiyan Liu, Zhiyong Zhang, Jianbin He, Yunyu Shi

About the Series

Chapman & Hall/CRC Mathematical and Computational Biology

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Subject Categories

BISAC Subject Codes/Headings:
MEDICAL / Biochemistry
SCIENCE / Chemistry / Physical & Theoretical