Reconstruction of protein backbones from the BriX collection of canonical protein fragments.

ABSTRACT: As modeling of changes in backbone conformation still lacks a computationally efficient solution, we developed a discretisation of the conformational states accessible to the protein backbone similar to the successful rotamer approach in side chains. The BriX fragment database, consisting of fragments from 4 to 14 residues long, was realized through identification of recurrent backbone fragments from a non-redundant set of high-resolution protein structures. BriX contains an alphabet of more than 1,000 frequently observed conformations per peptide length for 6 different variation levels. Analysis of the performance of BriX revealed an average structural coverage of protein structures of more than 99% within a root mean square distance (RMSD) of 1 Angstrom. Globally, we are able to reconstr

SUBMITTER: Baeten L 

PROVIDER: S-EPMC2367438 | biostudies-literature | 2008 May

REPOSITORIES: biostudies-literature