期刊
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
卷 2, 期 5, 页码 762-770出版社
WILEY PERIODICALS, INC
DOI: 10.1002/wcms.1099
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资金
- CASPUR (Consorzio Interuniversitario per le Applicazioni di Supercalcolo Per Universita e Ricerca)
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. (c) 2012 John Wiley & Sons, Ltd.
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