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Essential dynamics: foundation and applications
Author(s) -
Daidone Isabella,
Amadei Andrea
Publication year - 2012
Publication title -
wiley interdisciplinary reviews: computational molecular science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.126
H-Index - 81
eISSN - 1759-0884
pISSN - 1759-0876
DOI - 10.1002/wcms.1099
Subject(s) - subspace topology , molecular dynamics , foundation (evidence) , principal component analysis , computer science , energy landscape , folding (dsp implementation) , convergence (economics) , monte carlo method , statistical physics , principal (computer security) , motion (physics) , dynamics (music) , statistical mechanics , artificial intelligence , computational chemistry , physics , chemistry , mathematics , engineering , mechanical engineering , geography , statistics , archaeology , economic growth , acoustics , economics , thermodynamics , operating system
Collective coordinates, as obtained by a principal component analysis of atomic fluctuations, are commonly used to predict a low‐dimensional subspace in which essential protein motion is expected to take place. The definition of such an essential subspace allows to characterize protein functional, and folding, motion, to provide insight into the (free) energy landscape, and to enhance conformational sampling in molecular dynamics simulations. Here, we provide an overview on the topic, giving particular attention to some methodological aspects, such as the problem of convergence, and mentioning possible new developments. © 2012 John Wiley & Sons, Ltd. This article is categorized under: Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods