Hydrophobic residue-based superstructure

In the second stage, p-strands, p-sheets, and disulfide bridges are identified through a novel superstructure-based mathematical framework originally established for chemical process synthesis problems [121]. Two types of superstructure are introduced, both of which emanate from the principle that hydrophobic interactions drive the formation of p-stmcture. The first one, denoted as hydrophobic residue-based superstructure, encompasses all potential contacts between pairs of hydrophobic residues (i.e., a contact between two hydrophobic residues may or may not exist) that are not contained in helices (except cystines that are allowed to have cystine-cystine contacts even though they may be in hehces). The second one, denoted as -strand-based superstructure, includes all possible p-strand arrangements of interest (i.e., a p-strand may or may not exist) in addition to the potential contacts between hydrophobic residues. The hydrophobic residue-based and p-strand-based superstructures are... 

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