Structure. 2007 May;15(5):565-75.

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

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Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomèdica, Parc Cientific de Barcelona, 08028 Barcelona, Spain.

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.

PMID:: 17502102; [PubMed - indexed for MEDLINE]

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