Qiang Cui, Ivet Bahar
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.
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. All-atom normal mode calculations of large molecular systems using iterative methods. The Gaussian Network Model: Theory and Applications. Normal mode analysis of macromolecules: from enzyme activity site to molecular machines. Functional information from slow mode shapes. Unveiling Molecular Mechanisms of Biological Functions in Large Macromolecular Assemblies using Elastic Network Normal Mode Analysis. Applications of Normal Mode Analysis in Structural Refinement of Supramolecular Complexes. Normal Mode Analysis in Studying Protein Motions with X-ray Crystallography. Optimizing the Parameters of the Gaussian Network Model for ATP-Binding Proteins. Effects of Sequence, Cyclization, and Superhelical Stress on the Internet Motions of DNA. Symmetry in Normal Mode Analysis of Icosahedral Viruses. Extension of the normal mode concept: Principal component analysis, jumping-among-minimum model and their applications to experimental data analysis. 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. Probing vibrational energy relaxation in proteins using normal modes. Anharminic decay of vibrational state in proteins. Collective coordinate aproaches to extended conformational sampling. Using Collective coordinates to guide conformational sampling in atomic simulations.
Recent developments have enhanced the applicability of normal mode analysis (NMA) to macromolecular assemblies, solid states, and non-linear spectroscopes. This book provides comprehensive coverage of molecular structure and dynamics and their implications for biological and chemical function. It describes recent progress and potential future developments and covers both methodology and applications, including those involving large biomolecular complexes and novel MD and Monte Carlo simulations using concepts of NMA. Written by top researchers, the book complements traditional approaches with computational efficiency and applicability to large systems that are beyond the reach of older methods.
Inhaltsverzeichnis
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 T.Keyes 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
Klappentext
Recent developments have enhanced the applicability of normal mode analysis (NMA) to macromolecular assemblies, solid states, and non-linear spectroscopes. Normal Mode Analysis provides comprehensive coverage of molecular structure and dynamics and their implications for biological and chemical function. It describes recent progress and potential future developments and covers both methodology and applications, including those involving large biomolecular complexes and novel MD and Monte Carlo simulations using concepts of NMA. Written by top researchers in the field, the book complements traditional approaches with computational efficiency and applicability to large systems that are beyond the reach of older methods.
