Many important protein-protein interactions are mediated by peptide recognition domains (PRD), which bind short linear sequence motifs in other proteins. For example, SH3 domains typically recognize proline-rich motifs, PDZ domains recognize hydrophobic C-terminal tails, and kinases recognize short sequence regions around a phosphorylatable residue (Pawson, 2003).
Given the sequence of the domains, the challenge consists of predicting a position weight matrix (PWM) that describes the specificity profile of each of the given domains to their target peptides. Any publicly accessible peptide specificity information available for the domain may be used.
