NDLI: Using Fourier Spectrum Analysis and Pseudo Amino Acid Composition for Prediction of Membrane Protein Types

Content Provider	Springer Nature Link
Author	Liu, Hui Yang, Jie Wang, Meng Xue, Li Chou, Kuo Chen
Copyright Year	2005
Abstract	Membrane proteins are generally classified into the following five types: (1) type I membrane protein, (2) type II membrane protein, (3) multipass transmembrane proteins, (4) lipid chain-anchored membrane proteins, and (5) GPI-anchored membrane proteins. Given the sequence of an uncharacterized membrane protein, how can we identify which one of the above five types it belongs to? This is important because the biological function of a membrane protein is closely correlated with its type. Particularly, with the explosion of protein sequences entering into databanks, it is in high demand to develop an automated method to address this problem. To realize this, the key is to catch the statistical characteristics for each of the five types. However, it is not easy because they are buried in a pile of long and complicated sequences. In this paper, based on the concept of the pseudo amino acid composition (Chou, K. C. (2001). PROTEINS: Structure, Function, and Genetics 43: 246–255), the technique of Fourier spectrum analysis is introduced. By doing so, the sample of a protein is represented by a set of discrete components that can incorporate a considerable amount of the sequence order effects as well as its amino acid composition information. On the basis of such a statistical frame, the support vector machine (SVM) is introduced to perform predictions. High success rates were yielded by the self-consistency test, jackknife test, and independent dataset test, suggesting that the current approach holds a promising potential to become a high throughput tool for membrane protein type prediction as well as other related areas.
Starting Page	385
Ending Page	389
Page Count	5
File Format	PDF
ISSN	15723887
Journal	The Protein Journal
Volume Number	24
Issue Number	6
e-ISSN	15734943
Language	English
Publisher	Kluwer Academic Publishers-Plenum Publishers
Publisher Date	2005-01-01
Publisher Place	New York
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Discrete model Fourier spectrum analysis jackknife test pseudo amino acid composition support vector machines Organic Chemistry Biochemistry Animal Anatomy / Morphology / Histology Bioorganic Chemistry
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Analytical Chemistry Biochemistry Bioengineering

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