Thorough validation of protein normal mode analysis: a comparative study with essential dynamics.

TitleThorough validation of protein normal mode analysis: a comparative study with essential dynamics.
Publication TypeJournal Article
Year of Publication2007
AuthorsRueda, Manuel, Chacón Pablo, and Orozco Modesto
JournalStructure
Volume15
Pagination565-75
Date Published2007 May
ISSN0969-2126
KeywordsChemical, Computer Simulation, Models, Normal Distribution, Proteins, Thermodynamics
Abstract

The deformation patterns of a large set of representative proteins determined by essential dynamics extracted from atomistic simulations and coarse-grained normal mode analysis are compared. Our analysis shows that the deformational space obtained with both approaches is quite similar when taking into account a representative number of modes. The results provide not only a comprehensive validation of the use of a low-frequency modal spectrum to describe protein flexibility, but also a complete picture of normal mode limitations.

DOI10.1016/j.str.2007.03.013