Development of a rotamer library for use in beta-peptide foldamer computational design.

ABSTRACT: Foldamers present a particularly difficult challenge for accurate computational design compared to the case for conventional peptide and protein design due to the lack of a large body of structural data to allow parametrization of rotamer libraries and energies. We therefore explored the use of molecular mechanics for constructing rotamer libraries for non-natural foldamer backbones. We first evaluated the accuracy of molecular mechanics (MM) for the prediction of rotamer probability distributions in the crystal structures of proteins is explored. The van der Waals radius, dielectric constant and effective Boltzmann temperature were systematically varied to maximize agreement with experimental data. Boltzmann-weighted probabilities from these molecular mechanics energies compare well with

SUBMITTER: Shandler SJ 

PROVIDER: S-EPMC3079439 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature