Essentially there are two types of potentials that cater to two different sets of optimization methods. The more accurate potential functions score pair-interactions between amino acid residues in the protein (see Figure 6.2a). The residue pairs are grouped, for instance by the type of the two residues, their distance in the protein sequence, and their distance in the protein structure. E.g. residue A and L occurring at a distance of 6-15 residues apart in the protein sequence and at a distance between 3 A and 6 A in space may form such a group. The overall score of a sequence-structure alignment is the sum of all contributions determined by the inverse Boltzmann law of pairs of amino acids observed in the structure of the target sequence that is obtained by aligning the target sequence to the template structure as the alignment prescribes (see Figure 6.2). This kind of potential has been introduced by Sippl [30, 125].
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