title: PSOFuzzySVM-TMH: identification of transmembrane helix segments using ensemble feature space by incorporated fuzzy support vector machine.
abstract: Membrane protein is a central component of the cell that manages intra and extracellular processes. Membrane proteins execute a diversity of functions that are vital for the survival of organisms. The topology of transmembrane proteins describes the number of transmembrane (TM) helix segments and its orientation. However, owing to the lack of its recognized structures, the identification of TM helix and its topology through experimental methods is laborious with low throughput. In order to identify TM helix segments reliably, accurately, and effectively from topogenic sequences, we propose the PSOFuzzySVM-TMH model. In this model, evolutionary based information position specific scoring matrix and discrete based information 6-letter exchange group are used to formulate transmembrane protein sequences. The noisy and extraneous attributes are eradicated using an optimization selection technique, particle swarm optimization, from both feature spaces. Finally, the selected feature spaces are combined in order to form ensemble feature space. Fuzzy-support vector Machine is utilized as a classification algorithm. Two benchmark datasets, including low and high resolution datasets, are used. At various levels, the performance of the PSOFuzzySVM-TMH model is assessed through 10-fold cross validation test. The empirical results reveal that the proposed framework PSOFuzzySVM-TMH outperforms in terms of classification performance in the examined datasets. It is ascertained that the proposed model might be a useful and high throughput tool for academia and research community for further structure and functional studies on transmembrane proteins.
authors.affiliation: Department of Computer Science, Abdul Wali Khan University, Mardan, Pakistan. m.hayat@awkum.edu.pk maqsood.hayat@gmail.com.
authors.forename: Maqsood
authors.initials: M
authors.lastname: Hayat
authors.forename: Muhammad
authors.initials: M
authors.lastname: Tahir
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D017143:Fuzzy Logic; D008565:Membrane Proteins / Q000737:chemistry* / Q000235:genetics; D008962:Models, Theoretical; D056510:Position-Specific Scoring Matrices; D011487:Protein Conformation; D012984:Software; D060388:Support Vector Machine
chemical_list: D008565:Membrane Proteins