β-sheet topology prediction for β and mixed α/β proteins

BeST is a mixed-integer linear optimization based approach towards β-sheet prediction in β and mixed α/β proteins. The predicted beta sheet topology provides distance constraints between sequentially separated residues, which reduces the three dimensional search space for a structure prediction algorithm. 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-strand arrangements.