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

chapter 1|16 pages

Normal Mode Theory and Harmonic Potential Approximations

ByKonrad Hinsen

chapter 2|24 pages

All-Atom Normal Mode Calculations of Large Molecular Systems Using Iterative Methods

ByLiliane Mouawad, David Perahia

chapter 3|24 pages

The Gaussian Network Model: Theory and Applications

ByA.J. Rader, Chakra Chennubhotla, Lee-Wei Yang, and Ivet Bahar

chapter 4|26 pages

Normal Mode Analysis of Macromolecules: From Enzyme Active Sites to Molecular Machines

ByGuohui Li, Adam Van Wynsberghe, Omar N.A. Demerdash, and Qiang Cui

chapter 5|20 pages

Functional Information from Slow Mode Shapes

ByYves-Henri Sanejouand

chapter 8|16 pages

Normal Mode Analysis in Studying Protein Motions with X-Ray Crystallography

ByGeorge N. Phillips, Jr.

chapter 9|16 pages

Optimizing the Parameters of the Gaussian Network Model for ATP-Binding Proteins

ByTaner Z. Sen, Robert L. Jernigan

chapter 10|26 pages

Effects of Sequence, Cyclization, and Superhelical Stress on the Internal Motions of DNA

ByAtsushi Matsumoto, Wilma K. Olson

chapter 11|20 pages

Symmetry in Normal Mode Analysis of Icosahedral Viruses

ByHerman W.T. van Vlijmen

chapter 14|20 pages

Driven Molecular Dynamics for Normal Modes of Biomolecules without the Hessian, and Beyond

ByMartina Kaledin, Alexey L. Kaledin, Alex Brown, Joel M. Bowman

chapter 15|24 pages

Probing Vibrational Energy Relaxation in Proteins Using Normal

ByModes Hiroshi Fujisaki, Lintao Bu, John E. Straub

chapter 16|24 pages

Anharmonic Decay of Vibrational States in Proteins

ByXin Yu, David M. Leitner

chapter 17|18 pages

Collective Coordinate Approaches to Extended Conformational Sampling

ByMichael Nilges, Roger Abseher

chapter 18|22 pages

Using Collective Coordinates to Guide Conformational Sampling in Atomic Simulations

ByHaiyan Liu, Zhiyong Zhang, Jianbin He, Yunyu Shi