Enhanced Bounding Techniques to Reduce the Protein Conformational Search Space.

ABSTRACT: The complexity and enormous size of the conformational space that must be explored for the protein tertiary structure prediction problem has led to the development of a wide assortment of algorithmic approaches. In this study, we apply state-of-the-art tertiary structure prediction algorithms and instead focus on the development of bounding techniques to reduce the conformational search space. Dihedral angle bounds on the ϕ and ψ angles are established based on the predicted secondary structure and studies of the allowed regions of ϕ/ψ space. Distance bounds are developed based on predicted secondary structure information (including β-sheet topology predictions) to further reduce the search space. This bounding strategy is entirely independent of the degree of homology between the target p

SUBMITTER: McAllister SR 

PROVIDER: S-EPMC2903753 | biostudies-literature | 2009 Aug

REPOSITORIES: biostudies-literature