title: Strike: a protein-protein interaction classification approach.
abstract: Protein-protein interaction has proven to be a valuable biological knowledge and an initial point for understanding how the cell internally works. In this chapter, we introduce a novel approach termed STRIKE which uses String Kernel to predict protein-protein interaction. STRIKE classifies protein pairs into "interacting" and "non-interacting" sets based solely on amino acid sequence information. The classification is performed by applying the string kernel approach, which has been shown to achieve good performance on text categorization and protein sequence classification. Two proteins are classified as "interacting" if they contain similar substrings of amino acids. Strings' similarity would allow one to infer homology which could lead to a very similar structural relationship. To evaluate the performance of STRIKE, we apply it to classify into "interacting" and "non-interacting" protein pairs. The dataset of the protein pairs are generated from the yeast protein interaction literature. The dataset is supported by different lines of experimental evidence. STRIKE was able to achieve reasonable improvement over the existing protein-protein interaction prediction methods.
authors: Bioinformatics Laboratory, Department of Intelligent Systems, College of Information Technology, UAE University, 17551, Al-Ain, UAE. nzaki@uaeu.ac.ae
authors: Nazar
authors: N
authors: Zaki
authors: Wassim
authors: W
authors: El-Hajj
authors: Hesham M
authors: HM
authors: Kamel
authors: Fadi
authors: F
authors: Sibai
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology; D057225:Data Mining; D030562:Databases, Protein; D010363:Pattern Recognition, Automated; D054730:Protein Interaction Domains and Motifs / Q000235:genetics; D025941:Protein Interaction Mapping / Q000145:classification* / Q000706:statistics & numerical data*; D029701:Saccharomyces cerevisiae Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism; D012984:Software
chemical_list: D029701:Saccharomyces cerevisiae Proteins