title: The Topology Prediction of Membrane Proteins: A Web-Based Tutorial.
abstract: There is a great need for development of educational materials on the transfer of current bioinformatics knowledge to undergraduate students in bioscience departments. In this study, it is aimed to prepare an example in silico laboratory tutorial on the topology prediction of membrane proteins by bioinformatics tools. This laboratory tutorial is prepared for biochemistry lessons at bioscience departments (biology, chemistry, biochemistry, molecular biology and genetics, and faculty of medicine). The tutorial is intended for students who have not taken a bioinformatics course yet or already have taken a course as an introduction to bioinformatics. The tutorial is based on step-by-step explanations with illustrations. It can be applied under supervision of an instructor in the lessons, or it can be used as a self-study guide by students. In the tutorial, membrane-spanning regions and α-helices of membrane proteins were predicted by internet-based bioinformatics tools. According to the results achieved from internet-based bioinformatics tools, the algorithms and parameters used were effective on the accuracy of prediction. The importance of this laboratory tutorial lies on the facts that it provides an introduction to the bioinformatics and that it also demonstrates an in silico laboratory application to the students at natural sciences. The presented example education material is applicable easily at all departments that have internet connection. This study presents an alternative education material to the students in biochemistry laboratories in addition to classical laboratory experiments.
authors.affiliation: Department of Computer Science, Faculty of Science, Dokuz Eylül University, İzmir, Turkey.
authors.forename: Cagin
authors.initials: C
authors.lastname: Kandemir-Cavas
authors.affiliation: Division of Biochemistry, Department of Chemistry, Faculty of Science, Dokuz Eylül University, Kaynaklar Campus, 35160, İzmir, Turkey. levent.cavas@deu.edu.tr.
authors.forename: Levent
authors.initials: L
authors.lastname: Cavas
authors.affiliation: Institute of Marine Sciences and Technology, Dokuz Eylül University, 35340, İnciralti, İzmir, Turkey.
authors.forename: Hakan
authors.initials: H
authors.lastname: Alyuruk
mesh_terms: D000818:Animals; D001436:Bacteriorhodopsins / Q000737:chemistry; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D020407:Internet; D008565:Membrane Proteins / Q000737:chemistry*; D017433:Protein Structure, Secondary
chemical_list: D008565:Membrane Proteins; D001436:Bacteriorhodopsins
keywords: Biochemistry education; Bioinformatics tools; Laboratory tutorial; Protein topology; Transmembrane proteins