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

Normal Mode Analysis
Theory and Applications to Biological and Chemical Systems

Edited By

Qiang Cui


Ivet Bahar

ISBN 9781584884729
Published December 12, 2005 by Chapman & Hall
432 Pages 32 Color & 124 B/W Illustrations

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Book Description

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

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