Skip Navigation


PEDS Advance Access originally published online on September 22, 2009
Protein Engineering Design and Selection 2009 22(11):699-705; doi:10.1093/protein/gzp057
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Supplementary Data
Right arrow All Versions of this Article:
22/11/699    most recent
gzp057v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Lin, W.-Z.
Right arrow Articles by Chou, K.-C.
PubMed
Right arrow PubMed Citation
Right arrow Articles by Lin, W.-Z.
Right arrow Articles by Chou, K.-C.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org

GPCR-GIA: a web-server for identifying G-protein coupled receptors and their families with grey incidence analysis

Wei-Zhong Lin1, Xuan Xiao1,3 and Kuo-Chen Chou2

1Computer Department, Jing-De-Zhen Ceramic Institute, Jing-De-Zhen 333001, China 2 Gordon Life Science Institute, 13784 Torrey Del Mar Drive, San Diego, CA 92130, USA

3 To whom correspondence should be addressed. E-mail: xiaoxuan0326{at}yahoo.com.cn

G-protein-coupled receptors (GPCRs) play fundamental roles in regulating various physiological processes as well as the activity of virtually all cells. Different GPCR families are responsible for different functions. With the avalanche of protein sequences generated in the postgenomic age, it is highly desired to develop an automated method to address the two problems: given the sequence of a query protein, can we identify whether it is a GPCR? If it is, what family class does it belong to? Here, a two-layer ensemble classifier called GPCR-GIA was proposed by introducing a novel scale called ‘grey incident degree’. The overall success rate by GPCR-GIA in identifying GPCR and non-GPCR was about 95%, and that in identifying the GPCRs among their nine family classes was about 80%. These rates were obtained by the jackknife cross-validation tests on the stringent benchmark data sets where none of the proteins has ≥50% pairwise sequence identity to any other in a same class. Moreover, a user-friendly web-server was established at http://218.65.61.89:8080/bioinfo/GPCR-GIA. For user's convenience, a step-by-step guide on how to use the GPCR-GIA web server is provided. Generally speaking, one can get the desired two-level results in around 10 s for a query protein sequence of 300–400 amino acids; the longer the sequence is, the more time that is needed.

Keywords: ensemble classifier/fusion/K nearest neighbor algorithm/pseudo amino acid composition/web server

Received July 6, 2009; revised August 27, 2009; accepted August 27, 2009.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.