title: Conditional random field approach to prediction of protein-protein interactions using domain information.
abstract: BACKGROUND
  For understanding cellular systems and biological networks, it is important to analyze functions and interactions of proteins and domains. Many methods for predicting protein-protein interactions have been developed. It is known that mutual information between residues at interacting sites can be higher than that at non-interacting sites. It is based on the thought that amino acid residues at interacting sites have coevolved with those at the corresponding residues in the partner proteins. Several studies have shown that such mutual information is useful for identifying contact residues in interacting proteins.
  
  
  RESULTS
  We propose novel methods using conditional random fields for predicting protein-protein interactions. We focus on the mutual information between residues, and combine it with conditional random fields. In the methods, protein-protein interactions are modeled using domain-domain interactions. We perform computational experiments using protein-protein interaction datasets for several organisms, and calculate AUC (Area Under ROC Curve) score. The results suggest that our proposed methods with and without mutual information outperform EM (Expectation Maximization) method proposed by Deng et al., which is one of the best predictors based on domain-domain interactions.
  
  
  CONCLUSIONS
  We propose novel methods using conditional random fields with and without mutual information between domains. Our methods based on domain-domain interactions are useful for predicting protein-protein interactions.
authors.affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, Japan. morihiro@kuicr.kyoto-u.ac.jp
authors.forename: Morihiro
authors.initials: M
authors.lastname: Hayashida
authors.forename: Mayumi
authors.initials: M
authors.lastname: Kamada
authors.forename: Jiangning
authors.initials: J
authors.lastname: Song
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Akutsu
mesh_terms: D000818:Animals; D019540:Area Under Curve; D029742:Caenorhabditis elegans Proteins / Q000737:chemistry / Q000378:metabolism; D029721:Drosophila Proteins / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D011336:Probability; D025941:Protein Interaction Mapping / Q000379:methods*; D017434:Protein Structure, Tertiary; D013269:Stochastic Processes
chemical_list: D029742:Caenorhabditis elegans Proteins; D029721:Drosophila Proteins