Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling.

ABSTRACT: We report the development of internal coordinate mechanics force field (ICMFF), new force field parameterized using a combination of experimental data for crystals of small molecules and quantum mechanics calculations. The main features of ICMFF include: (a) parameterization for the dielectric constant relevant to the condensed state (ε = 2) instead of vacuum, (b) an improved description of hydrogen-bond interactions using duplicate sets of van der Waals parameters for heavy atom-hydrogen interactions, and (c) improved backbone covalent geometry and energetics achieved using novel backbone torsional potentials and inclusion of the bond angles at the C(α) atoms into the internal variable set. The performance of ICMFF was evaluated through loop modeling simulations for 4-13 residue loops. IC

SUBMITTER: Arnautova YA 

PROVIDER: S-EPMC3057902 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature