Residue-based contact interaction potential

As methods based on dynamic programming cannot account for pairwise-interaction potentials the so-called frozen approximation approach [189] has been proposed. This method performs several iterations of profile environments. In the first iteration, the chemical environment is defined via the contact partners of the template. In subsequent rounds the aligned residues from the previous iteration replace the residues of the template. The idea is that target and template structure are similar enough such that the iterative process converges towards the optimal assignment. 

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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