Thorough validation of protein normal mode analysis: a comparative study with essential dynamics.
Title | Thorough validation of protein normal mode analysis: a comparative study with essential dynamics. |
Publication Type | Journal Article |
Year of Publication | 2007 |
Authors | Rueda, Manuel, Chacón Pablo, and Orozco Modesto |
Journal | Structure |
Volume | 15 |
Pagination | 565-75 |
Date Published | 2007 May |
ISSN | 0969-2126 |
Keywords | Chemical, 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. |
DOI | 10.1016/j.str.2007.03.013 |