1 Normal Mode Theory and Harmonic Potential Approximations 1
Konrad Hinsen
2 All-Atom Normal Mode Calculations of Large Molecular Systems
Using Iterative Methods 17
Liliane Mouawad and David Perahia
3 The Gaussian Network Model: Theory and Applications 41
A.J. Rader, Chakra Chennubhotla, Lee-Wei Yang, and Ivet Bahar
4 Normal Mode Analysis of Macromolecules: From Enzyme Active
Sites to Molecular Machines 65
Guohui Li, Adam Van Wynsberghe, Omar N.A. Demerdash, and
Qiang Cui
5 Functional Information from Slow Mode Shapes 91
Yves-Henri Sanejouand
6 Unveiling Molecular Mechanisms of Biological Functions in Large
Macromolecular Assemblies Using Elastic Network Normal
Mode Analysis 111
Florence Tama and Charles L. Brooks III
7 Applications of Normal Mode Analysis in Structural Refinement
of Supramolecular Complexes 137
Jianpeng Ma
8 Normal Mode Analysis in Studying Protein Motions with X-Ray
Crystallography 155
George N. Phillips, Jr.
9 Optimizing the Parameters of the Gaussian Network Model for
ATP-Binding Proteins 171
Taner Z. Sen and Robert L. Jernigan
10 Effects of Sequence, Cyclization, and Superhelical Stress on the
Internal Motions of DNA 187
Atsushi Matsumoto and Wilma K. Olson
11 Symmetry in Normal Mode Analysis of Icosahedral Viruses 213
Herman W.T. van Vlijmen
12 Extension of the Normal Mode Concept: Principal Component
Analysis, Jumping-Among-Minima Model, and Their
Applications to Experimental Data Analysis 233
Akio Kitao
13 Imaginary-Frequency, Unstable Instantaneous Normal Modes,
the Potential Energy Landscape, and Diffusion in Liquids 253
T. Keyes
14 Driven Molecular Dynamics for Normal Modes of Biomolecules
without the Hessian, and Beyond 281
Martina Kaledin, Alexey L. Kaledin, Alex Brown, and Joel M. Bowman
15 Probing Vibrational Energy Relaxation in Proteins Using Normal
Modes 301
Hiroshi Fujisaki, Lintao Bu, and John E. Straub
16 Anharmonic Decay of Vibrational States in Proteins 325
Xin Yu and David M. Leitner
17 Collective Coordinate Approaches to Extended Conformational
Sampling 349
Michael Nilges and Roger Abseher
18 Using Collective Coordinates to Guide Conformational Sampling
in Atomic Simulations 367
Haiyan Liu, Zhiyong Zhang, Jianbin He, and Yunyu Shi