title: PPIevo: protein-protein interaction prediction from PSSM based evolutionary information.
abstract: Protein-protein interactions regulate a variety of cellular processes. There is a great need for computational methods as a complement to experimental methods with which to predict protein interactions due to the existence of many limitations involved in experimental techniques. Here, we introduce a novel evolutionary based feature extraction algorithm for protein-protein interaction (PPI) prediction. The algorithm is called PPIevo and extracts the evolutionary feature from Position-Specific Scoring Matrix (PSSM) of protein with known sequence. The algorithm does not depend on the protein annotations, and the features are based on the evolutionary history of the proteins. This enables the algorithm to have more power for predicting protein-protein interaction than many sequence based algorithms. Results on the HPRD database show better performance and robustness of the proposed method. They also reveal that the negative dataset selection could lead to an acute performance overestimation which is the principal drawback of the available methods.
authors.affiliation: Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
authors.forename: Javad
authors.initials: J
authors.lastname: Zahiri
authors.forename: Omid
authors.initials: O
authors.lastname: Yaghoubi
authors.forename: Morteza
authors.initials: M
authors.lastname: Mohammad-Noori
authors.forename: Reza
authors.initials: R
authors.lastname: Ebrahimpour
authors.forename: Ali
authors.initials: A
authors.lastname: Masoudi-Nejad
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001185:Artificial Intelligence; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D019143:Evolution, Molecular; D006801:Humans; D010802:Phylogeny; D056510:Position-Specific Scoring Matrices; D060066:Protein Interaction Maps; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D011506:Proteins
keywords: Computational intelligence; Machine learning; Position-specific scoring matrix; Protein interaction networks; Protein–protein interaction map