An Iterative Approach to Class II Predictions
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An iterative approach to resolving protein–peptide binding motifs is appropriate when the length of the binding protein is variable and a variety of amino acid residues may successfully occupy multiple positions. This chapter describes an iterative algorithm that first aligns binding peptides of variable lengths and then extracts a quantitative motif from the resulting alignment. Numerous examples are presented to illustrate the utility of the iterative process.
