Essential dynamics: foundation and applications

• DOI: 10.1002/wcms.1099
• Publication Date: 2012-02-29T20:08:51Z
• Authors: Isabella Daidone; Andrea Amadei
• Keywords: Foundation (evidence); Energy landscape; Folding (DSP implementation); Dynamics; Statistical Mechanics

Abstract Collective coordinates, as obtained by a principal component analysis of atomic fluctuations, are commonly used to predict low‐dimensional subspace in which essential protein motion is expected take place. The definition such an allows characterize functional, and folding, motion, provide insight into the (free) energy landscape, enhance conformational sampling molecular dynamics simulations. Here, we overview on topic, giving particular attention some methodological aspects, problem convergence, mentioning possible new developments. © 2012 John Wiley & Sons, Ltd. This article categorized under: Molecular Statistical Mechanics > Dynamics Monte-Carlo Methods