β-sheet topology prediction with high precision and recall for β and mixed α/β proteins.

ABSTRACT: The prediction of the correct β-sheet topology for pure β and mixed α/β proteins is a critical intermediate step toward the three dimensional protein structure prediction. The predicted beta sheet topology provides distance constraints between sequentially separated residues, which reduces the three dimensional search space for a protein structure prediction algorithm. Here, we present a novel mixed integer linear optimization based framework for the prediction of β-sheet topology in β and mixed α/β proteins. The objective is to maximize the total strand-to-strand contact potential of the protein. A large number of physical constraints are applied to provide biologically meaningful topology results. The formulation permits the creation of a rank-ordered list of preferred β-sheet arrangemen

SUBMITTER: Subramani A 

PROVIDER: S-EPMC3302896 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature