Fig. 2.

Example of an assignment of the β-sheet topology for a protein with five β-strands. (a) The weight matrix S of the integer programming optimization. Each element of S corresponds to the strand interaction score. Strands interaction scores may be derived from parallel (upper diagonal part of the matrix) or antiparallel (lower diagonal part of the matrix) strand alignments. (b) The assigned β-sheet topology {(1,3,A), (1,5,A), (2,4,P), (2,5,A)} (A = antiparallel, P = parallel) obtained from the integer program solution and corresponding strand pairing directions