Normal Mode Analysis is a simulation technique used to sudy vibrational motion of a harmonic oscillating system in the vicinity of its equilibrium. NMA is increasingly used to study slow dynamics of biomolecules. NMA is better suited for probing large-scale conformational motions in proteins which are otherwise computationally demanding to be sampled by MD simulations.
A normal mode corresponds to a resonant motion where all the components of a system are moving with the same frequency and in phase. Normal mode analysis (also termed as harmonic analysis) is based on the assumption that the normal modes with the lowest frequencies are the functionally most relevant modes and they describe the large-scale, overall motion of the protein. In addition to exploring the functional motions of a protein, NMA can also be used to study the transition paths between two conformations of a protein or to improve protein-ligand docking calculations.
To read more about Normal Mode Analysis and its application to Biomolecules, please refer to the following papers:
1. Skjaerven L, Hollup SM, Reuter N. Normal mode analysis for proteins. J Mol Struct THEOCHEM. 2009;898: 42–48.
2. Bahar I, Lezon TR, Bakan A, Shrivastava IH. Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins. Chemical reviews. 2010;110(3):1463-1497.
Normal Mode Analysis (NMA) can be performed using the following software tools:
For examples of previously performed studies in which Normal Mode Analysis (NMA) was the primary method used, see the following example cases: