title: Identification of mycobacterial membrane proteins and their types using over-represented tripeptide compositions.
abstract: Mycobacterium can cause many serious diseases, such as tuberculosis and leprosy. Its membrane proteins play a critical role for multidrug-resistance and its tenacious survival ability. Knowing the types of membrane proteins will provide novel insights into understanding their functions and facilitate drug target discovery. In this study, a novel method was developed for predicting mycobacterial membrane protein and their types by using over-represented tripeptides. A total of 295 non-membrane proteins and 274 membrane proteins were collected to evaluate the performance of proposed method. The results of jackknife cross-validation test show that our method achieves an overall accuracy of 93.0% in discriminating between mycobacterial membrane proteins and mycobacterial non-membrane proteins and an overall accuracy of 93.1% in classifying mycobacterial membrane protein types. By comparing with other methods, the proposed method showed excellent predictive performance. Based on the proposed method, we built a predictor, called MycoMemSVM, which is freely available at http://lin.uestc.edu.cn/server/MycoMemSVM. It is anticipated that MycoMemSVM will become a useful tool for the annotation of mycobacterial membrane proteins and the development of anti-mycobacterium drug design.
authors.affiliation: Key Laboratory for NeuroInformation of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
authors.forename: Chen
authors.initials: C
authors.lastname: Ding
authors.forename: Lu-Feng
authors.initials: LF
authors.lastname: Yuan
authors.forename: Shou-Hui
authors.initials: SH
authors.lastname: Guo
authors.forename: Hao
authors.initials: H
authors.lastname: Lin
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D030562:Databases, Protein; D008565:Membrane Proteins / Q000235:genetics* / Q000378:metabolism; D009161:Mycobacterium / Q000235:genetics* / Q000378:metabolism; D009164:Mycobacterium Infections / Q000188:drug therapy / Q000235:genetics* / Q000378:metabolism; D009842:Oligopeptides / Q000235:genetics* / Q000378:metabolism; D020539:Sequence Analysis, Protein / Q000379:methods
chemical_list: D001426:Bacterial Proteins; D008565:Membrane Proteins; D009842:Oligopeptides