Cytoprophet is a project developed by the Laboratory for Computational Life Sciences at the Computer Science Department of the University of Notre Dame. It is a tool to help researchers to infer new potential protein (PPI) and domain (DDI) interactions. It is implemented as a Cytoscape plugin, where users input a set of proteins and retrieve a network of plausible protein and domain interactions with a score. Three algorithms are used for the estimation of PPI/DDI: Maximum Specificity Set Cover (MSSC) Approach, Maximum Likelihood Estimation (MLE) and the Sum-Product Algorithm (SPA) for protein networks.
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Chengbang Huang , Faruck Morcos, Simon P. Kanaan, Stefan Wuchty, Danny Z. Chen, and Jesús A. Izaguirre
Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol 4 pp. 78-87. Jan-March 2007