Identifying the residues in a protein that are involved in protein-protein interaction and identifying the contact\nmatrix for a pair of interacting proteins are two computational tasks at different levels of an in-depth analysis of\nprotein-protein interaction. Various methods for solving these two problems have been reported in the literature.\nHowever, the interacting residue prediction and contact matrix prediction were handled by and large independently in\nthose existing methods, though intuitively good prediction of interacting residues will help with predicting the contact\nmatrix. In this work, we developed a novel protein interacting residue prediction system, contact matrix-interaction\nprofile hidden Markov model (CM-ipHMM), with the integration of contact matrix prediction and the ipHMM\ninteraction residue prediction. We propose to leverage what is learned from the contact matrix prediction and\nutilize the predicted contact matrix as ââ?¬Å?feedbackââ?¬Â to enhance the interaction residue prediction. The CM-ipHMM\nmodel showed significant improvement over the previous method that uses the ipHMM for predicting interaction\nresidues only. It indicates that the downstream contact matrix prediction could help the interaction site prediction.
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