MDCinfer aims to infer protein-protein interaction by considering cooperative domain interactions. Unlike most existing methods, it assumes cooperative-domain pairs but not only single-domain pairs as the basic units of a protein interaction. The interaction probabilities of single-domain pairs and cooperative-domain pairs are computed by a linear programming algorithm and a fast association probabilistic method. Novel protein interactions can be predicted by an extended probabilities model which can accommodate cooperative-domain pairs.
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Rui-Sheng Wang, Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, and Luonan Chen.
Analysis on multi-domain cooperation for predicting protein-protein interactions.
BMC Bioinformatics, Vol. 8, 391, 2007.