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