Normal mode analysis : theory and applications to biological and chemical systems

By Qiang Cui, Ivet Bahar. 2005

346 citations recorded by the source corpus.

Subfields: Molecular Biology, Physical and Theoretical Chemistry, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/3bd76a44737e79976cdfcea5210f8e8fcbe84982

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. Debashish Chowdhury
2. Eran Eyal
3. Lee-Wei Yang
4. Ivet Bahar
5. Qiang Cui
6. Timothy R. Lezon
7. Charles C. David
8. David J. Fleet

In Physical and Theoretical Chemistry

1. Eran Eyal
2. Lee-Wei Yang
3. Debashish Chowdhury
4. Ivet Bahar
5. Qiang Cui

In Spectroscopy

1. Eran Eyal
2. Lee-Wei Yang
3. Debashish Chowdhury
4. Ivet Bahar
5. Martin Karplus
6. Qiang Cui

Citations in the corpus

• Allostery and cooperativity revisited (2008, background): “This has been demonstrated explicitly by normal mode studies (Cui and Bahar 2006), which show that the functional motions are generally well described by a few lowfrequency modes (Cui et al. 2004).”
• 3D Variability Analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM (2020, background): “Techniques like normal-modes analysis [4] make assumptions about the energy landscape and dynamics of a protein molecule to predict possible flexibility.”
• Persistent homology analysis of protein structure, flexibility and folding (2014, neutral): “A more detailed description is available from review literature [75–78].”
• Anisotropic network model: systematic evaluation and a new web interface (2006, methodology): “The major utility of ANM calculations, or NMAs with EN models in general , is not, however, to compute the mean-square fluctuations of amino acids, which can be obtained from experiments (or computed by simpler methods such as the GNM).”
• Principal Component Analysis: A Method for Determining the Essential Dynamics of Proteins (2014, background): “Since proteins display a significant amount of anharmonicity in their behavior [19, 20], this assumption is not always suitable [21–23].”
• iMod: multipurpose normal mode analysis in internal coordinates (2011, neutral): “Normal mode analysis (NMA) merged with coarse-grained (CG) models has proven to be a powerful and popular alternative to simulate collective motions of macromolecular complexes at extended timescales (Bahar and Rader, 2005; Bahar et al., 2010; Cui and Bahar, 2007; Ma, 2005; Skjaerven et al., 2009; T”
• Stochastic mechano-chemical kinetics of molecular motors: A multidisciplinary enterprise from a physicist’s perspective (2012, background): “However, some insight into the conformational dynamics of the motor can be gained by carying out the standard normal mode analysis (NMA) [386] of a fully atomistic model.”
• Global dynamics of proteins: bridging between structure and function. (2010, background): “Recent years have witnessed an explosion in the number of studies that use elastic network models (ENMs) and normal mode analysis (NMA) for exploring the structure-encoded dynamics that depends exclusively on native contact topology (8, 17).”