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  • Title: Inferring protein function by domain context similarities in protein-protein interaction networks.
    Author: Zhang S, Chen H, Liu K, Sun Z.
    Journal: BMC Bioinformatics; 2009 Dec 02; 10():395. PubMed ID: 19954509.
    Abstract:
    BACKGROUND: Genome sequencing projects generate massive amounts of sequence data but there are still many proteins whose functions remain unknown. The availability of large scale protein-protein interaction data sets makes it possible to develop new function prediction methods based on protein-protein interaction (PPI) networks. Although several existing methods combine multiple information resources, there is no study that integrates protein domain information and PPI networks to predict protein functions. RESULTS: The domain context similarity can be a useful index to predict protein function similarity. The prediction accuracy of our method in yeast is between 63%-67%, which outperforms the other methods in terms of ROC curves. CONCLUSION: This paper presents a novel protein function prediction method that combines protein domain composition information and PPI networks. Performance evaluations show that this method outperforms existing methods.
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