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Functional Dynamics of Proteins Elucidated by Statistical Analysis of Simulation Data

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Conformational dynamics and flexibility form the link between protein structure and function. Molecular dynamics (MD) simulations have been valuable for our understanding of conformational energy landscape and protein dynamics at the atomic scale, which is difficult to probe experimentally. In this respect, the essential dynamics of proteins revealed by principal component analysis of MD simulation data provide information on functional motions that generally bear a collective nature. In this review, we summarize literature on statistical analysis of MD data with an emphasis on recent promising methods that can be applied to study the effect of ligand binding.
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Keywords: Collective motions; Ligand binding; Molecular dynamics simulations; Nonlinear dynamics; Principal component analysis; Time series model

Document Type: Research Article

Publication date: December 1, 2012

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  • Current Physical Chemistry publishes full-length and short reviews, and topical issues on the important recent developments in physical chemistry and allied disciplines.The scope of the journal covers all areas of physical chemistry, including surface science, colloids and interfaces, thermodynamics, spectroscopy, molecular structure, solid state chemistry, catalysis, kinetics, theoretical chemistry, chemical physics and biophysical chemistry.Current Physical Chemistry is an essential journal for every physical chemist who wishes to be kept informed and up-to-date with the latest and most important developments.
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