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About this book
About this book
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.
Normal mode theory and harmonic potential approximationsKonrad HinsenAll-atom normal mode calculations of large molecular systems using iterative methodsLiliane Mouawad and David PerahiaThe Gaussian network model: Theory and applicationsA.J. Radar, Chakra Chennubhotla, Lee-Wei Yang, Ivet BaharNormal mode analysis of macromolecules: from enzyme activity site to molecular machinesGuohui Li, Adam Van Wynsbergh, Omar N.A. Demerdash, Qiang CuiFunctional information from slow mode shapesYves-Henri SanejouandUnveiling molecular mechanisms of biological functions in large macromolecular assemblies using elastic network normal mode analysisFlorence Tama, Charles L. Brooks IIIApplications of normal mode analysis in structural refinement of supramolecular complexesJianpeng MaNormal mode analysis in studying protein motions with x-ray crystallographyGeorge N. Phillips, Jr.Optimizing the parameters of the Gaussian network model for ATP-binding proteinsTaner Z. Sen, Robert L. JerniganEffects of sequence, cyclization, and superhelical stress on the internet motions of DNAAtsushi Matsumoto, Wilma K. OlsonSymmetry in normal mode analysis of icosahedral virusesHerman W.T. van VlijmenExtension of the normal mode concept: Principal component analysis, jumping-among-minima model, and their applications to experimental data analysisAkio KitaoImaginary-frequency, unstable instantaneous normal modes, the potential energy landscape, and diffusion in liquidsT.KeyesDriven molecular dynamics for normal modes of biomolecules without the Hessian, and beyondMartina Kaledin, Alexey L. Kaledin, Alex Brown, and Joel BowmanProbing vibrational energy relaxation in proteins using normal modesHiroshi Fujisaki, Lintao Bu, and John E. StraubAnharmonic decay of vibrational state in proteinsXin Yu, David M. LeitnerCollective coordinate approaches to extended conformational samplingMichael Nilges, Rogher AbseherUsing collective coordinates to guide conformational sampling in atomic simulationsHaiyan Liu, Zhiyong Zhang, Jianbin He, Yunyu Shi