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Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to
P Doruker1, A R Atilgan, I Bahar
1Polymer Research Center, School of Engineering, Bogazici University, and TUBITAK Advanced Polymeric Materials Research Center, Bebek, Istanbul, Turkey.
Proteins
|June 22, 2000
Abstract:
The dynamics of alpha-amylase inhibitors has been investigated using molecular dynamics (MD) simulations and two analytical approaches, the Gaussian network model (GNM) and anisotropic network model (ANM). MD simulations use a full atomic approach with empirical force fields, while the analytical approaches are based on a coarse-grained single-site-per-residue model with a single-parameter harmonic potential between sufficiently close (r