fSUB: Normal Mode Analysis with Flexible Substructures
نویسندگان
چکیده
منابع مشابه
Normalizing normal mode analysis.
Few would disagree, but a generation later, the statement remains a prophecy rather than fact. Although 41,000 protein structures are known, there are none for which there is a complete description of the dynamics that is often key to understanding functional mechanism. Despite keen interest in protein dynamics, studies have remained the purview of computer simulation while the challenges of ex...
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In this paper, we consider a flexible skew-generalized normal distribution. This distribution is denoted by $FSGN(/lambda _1, /lambda _2 /theta)$. It contains the normal, skew-normal (Azzalini, 1985), skew generalized normal (Arellano-Valle et al., 2004) and skew flexible-normal (Gomez et al., 2011) distributions as special cases. Some important properties of this distribution are establi...
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The dynamic simulation of macromolecular systems with biologically relevant sizes and time scales is critical for understanding macromolecular function. In this context, normal mode analysis (NMA) approximates the complex dynamicalbehaviourofa macromoleculeas a simple setof harmonic oscillators vibrating around a given equilibrium conformation. This technique, originated from classical mechanic...
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With the increased popularity of normal mode analyses in structural biology, it is important to carefully consider how to best utilize the results for gaining biological insights without over interpretation. The discussion in this article argues that for the purpose of identifying correlated motions in biomolecules, a case separate from concomitant conformational changes of structural motifs, i...
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Normal mode analysis (NMA) in internal (dihedral) coordinates naturally reproduces the collective functional motions of biological macromolecules. iMODS facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures, even with large macromolecules. The distinctive internal coordinate formulation improves the efficiency of NMA and extends i...
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ژورنال
عنوان ژورنال: The Journal of Physical Chemistry B
سال: 2012
ISSN: 1520-6106,1520-5207
DOI: 10.1021/jp300312u