Thorough validation of protein normal mode analysis: a comparative study with essential dynamics.
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.
Rueda
Manuel
M
Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomèdica, Parc Cientific de Barcelona, 08028 Barcelona, Spain.
Chacón
Pablo
P
Orozco
Modesto
M
D003198:Computer Simulation; D008956:Models, Chemical; D016011:Normal Distribution; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D011506:Proteins