ProtRet: A Web Server for Retrieving Proteins in a Functional Complex
The identification of protein complexes is becoming increasingly important to our understanding of cellular functionality. However, if a biologist wishes to investigate a certain protein, currently no method exists to assist him/her to accurately retrieve the possible protein partners that are expected to be in the same functional complex. Here, we introduce ProtRet, a web server that functions as an interface for an improved Pigeonhole approach to identify protein complexes in protein-protein interaction networks. The approach provides high-quality protein comparison that is particularly valuable because of its accurate statistical estimates based on fuzzy criterion and Hamming distance. The proposed method was tested on two high-throughput experimental protein-protein interaction data sets and two gold standard data sets and was able to retrieve more correct protein members than all existing methods. The web server is accessible from the link http://www.protret.com/.
KeywordsProtein complexes Protein-protein interaction Pigeonhole method Information retrieval
The authors acknowledge financial support from the ICT Fund (Grant # G00001472) and the UAEU (Grant # G00002659).
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