Paper Citing NAMD - Abstract
Rueda, Manuel; Chacon, Pablo; Orozco, Modesto
Thorough validation of protein normal mode analysis: A comparative study with essential dynamics
STRUCTURE, 15:565-575, MAY 2007
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.
