[HTML][HTML] Thorough validation of protein normal mode analysis: a comparative study with essential dynamics

M Rueda, P Chacón, M Orozco - Structure, 2007 - cell.com
Structure, 2007cell.com
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 …
Summary
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.
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