Optimal Coarse-Grained Site Selection in Elastic Network Models of Biomolecules.

ABSTRACT: Elastic network models, simple structure-based representations of biomolecules where atoms interact via short-range harmonic potentials, provide great insight into a molecule's internal dynamics and mechanical properties at extremely low computational cost. Their efficiency and effectiveness have made them a pivotal instrument in the computer-aided study of proteins and, since a few years, also of nucleic acids. In general, the coarse-grained sites, i.e. those effective force centers onto which the all-atom structure is mapped, are constructed based on intuitive rules: a typical choice for proteins is to retain only the C _α atoms of each amino acid. However, a mapping strategy relying only on the atom type and not the local properties of its embedding can be suboptimal compared

SUBMITTER: Diggins P 

PROVIDER: S-EPMC6391041 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature