1st Edition

Normal Mode Analysis Theory and Applications to Biological and Chemical Systems

Edited By Qiang Cui, Ivet Bahar Copyright 2006
    430 Pages 32 Color & 124 B/W Illustrations
    by Chapman & Hall

    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.

    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


    Qiang Cui, Ivet Bahar