Protein-protein interactions play a central role in many cellular functions, and as whole-genome data accumulates, computational methods for predicting these interactions become increasingly important. Computational methods have already proven to be auseful first step for rapid genome-wide identification of putative protein structure and function, but research on the problem of computationally determining biologically relevant partners for given protein sequences is just beginning. In this paper, weapproach the problem of predicting protein-protein interactions by focusing on the 2-stranded coiled-coil motif. We introduce a computational method for predicting coiled-coil protein interactions, and give a novel framework that is able to use both genomic sequence data and experimental data in making these predictions. Cross-validation tests show that the method is able to predict many aspects of protein-protein interactions mediated by the coiled-coil motif, and suggest that this methodology can beused as the basis for genome-wide prediction of coiled-coil protein interactions.
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