title: Application of wavelet transform for PDZ domain classification.
abstract: PDZ domains have been identified as part of an array of signaling proteins that are often unrelated, except for the well-conserved structural PDZ domain they contain. These domains have been linked to many disease processes including common Avian influenza, as well as very rare conditions such as Fraser and Usher syndromes. Historically, based on the interactions and the nature of bonds they form, PDZ domains have most often been classified into one of three classes (class I, class II and others - class III), that is directly dependent on their binding partner. In this study, we report on three unique feature extraction approaches based on the bigram and trigram occurrence and existence rearrangements within the domain's primary amino acid sequences in assisting PDZ domain classification. Wavelet packet transform (WPT) and Shannon entropy denoted by wavelet entropy (WE) feature extraction methods were proposed. Using 115 unique human and mouse PDZ domains, the existence rearrangement approach yielded a high recognition rate (78.34%), which outperformed our occurrence rearrangements based method. The recognition rate was (81.41%) with validation technique. The method reported for PDZ domain classification from primary sequences proved to be an encouraging approach for obtaining consistent classification results. We anticipate that by increasing the database size, we can further improve feature extraction and correct classification.
authors: Electrical and Computer Engineering Department, Faculty of Engineering, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
authors: Khaled
authors: K
authors: Daqrouq
authors: Electrical and Computer Engineering Department, Faculty of Engineering, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
authors: Rami
authors: R
authors: Alhmouz
authors: Electrical and Computer Engineering Department, Faculty of Engineering, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
authors: Ahmed
authors: A
authors: Balamesh
authors: Center of Nanotechnology, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
authors: Adnan
authors: A
authors: Memic
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D030562:Databases, Protein; D019277:Entropy; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D054731:PDZ Domains; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D058067:Wavelet Analysis
chemical_list: D011506:Proteins