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On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations

✍ Scribed by Andrea Amadei; Marc A. Ceruso; Alfredo Di Nola

Publisher: John Wiley and Sons
Year: 1999
Tongue: English
Weight: 119 KB
Volume: 36
Category: Article
ISSN: 0887-3585
DOI: 10.1002/(sici)1097-0134(19990901)36:4<419::aid-prot5>3.0.co;2-u

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✦ Synopsis

In this article we present a quantitative evaluation of the convergence of the conformational coordinates of proteins, obtained by the Essential Dynamics method. Using a detailed analysis of long molecular dynamics trajectories in combination with a statistical assessment of the significance of the measured convergence, we obtained that simulations of a few hundreds of picoseconds are in general sufficient to provide a stable and statistically reliable definition of the essential and near constraints subspaces, at least within the nanoseconds time range.

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