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|
|Date Published||2007 May|
|Keywords||Chemical, Computer Simulation, Models, Normal Distribution, Proteins, Thermodynamics|
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.