Jump to main content
Jump to site search

Issue 3, 2011
Previous Article Next Article

GPCR-2L: predicting G protein-coupled receptors and their types by hybridizing two different modes of pseudo amino acid compositions

Author affiliations

Abstract

G protein-coupled receptors (GPCRs) are among the most frequent targets of therapeutic drugs. With the avalanche of newly generated protein sequences in the post genomic age, to expedite the process of drug discovery, it is highly desirable to develop an automated method to rapidly identify GPCRs and their types. A new predictor was developed by hybridizing two different modes of pseudo-amino acid composition (PseAAC): the functional domain PseAAC and the low-frequency Fourier spectrum PseAAC. The new predictor is called GPCR-2L, where “2L” means that it is a two-layer predictor: the 1st layer prediction engine is to identify a query protein as GPCR or not; if it is, the prediction will be automatically continued to further identify it as belonging to one of the following six types: (1) rhodopsin-like (Class A), (2) secretin-like (Class B), (3) metabotropic glutamate/pheromone (Class C), (4) fungal pheromone (Class D), (5) cAMP receptor (Class E), or (6) frizzled/smoothened family (Class F). The overall success rate of GPCR-2L in identifying proteins as GPCRs or non-GPCRs is over 97.2%, while identifying GPCRs among their six types is over 97.8%. Such high success rates were derived by the rigorous jackknife cross-validation on a stringent benchmark dataset, in which none of the included proteins had ≥40% pairwise sequence identity to any other protein in a same subset. As a user-friendly web-server, GPCR-2L is freely accessible to the public at http://icpr.jci.edu.cn/bioinfo/GPCR-2L, by which one can obtain the 2-level results in about 20 s for a query protein sequence of 500 amino acids. The longer the sequence is, the more time it may usually need. The high success rates reported here indicate that it is a quite effective approach to identify GPCRs and their types with the functional domain information and the low-frequency Fourier spectrum analysis. It is anticipated that GPCR-2L may become a useful tool for both basic research and drug development in the areas related to GPCRs.

Graphical abstract: GPCR-2L: predicting G protein-coupled receptors and their types by hybridizing two different modes of pseudo amino acid compositions

Back to tab navigation

Supplementary files

Publication details

The article was received on 20 Aug 2010, accepted on 18 Nov 2010 and first published on 23 Dec 2010


Article type: Paper
DOI: 10.1039/C0MB00170H
Citation: Mol. BioSyst., 2011,7, 911-919
  •   Request permissions

    GPCR-2L: predicting G protein-coupled receptors and their types by hybridizing two different modes of pseudo amino acid compositions

    X. Xiao, P. Wang and K. Chou, Mol. BioSyst., 2011, 7, 911
    DOI: 10.1039/C0MB00170H

Search articles by author

Spotlight

Advertisements