GPCRsclass: a web tool for the classification of amine type of G-protein-coupled receptors.
The receptors of amine subfamily are specifically major drug targets for therapy of nervous disorders and psychiatric diseases. The recognition of novel amine type of receptors and their cognate ligands is of paramount interest for pharmaceutical companies. In the past, Chou and co-workers have shown that different types of amine receptors are correlated with their amino acid composition and are predictable on its basis with considerable accuracy [Elrod and Chou (2002) Protein Eng., 15, 713-715]. This motivated us to develop a better method for the recognition of novel amine receptors and for their further classification. The method was developed on the basis of amino acid composition and dipeptide composition of proteins using support vector machine. The method was trained and tested on 167 proteins of amine subfamily of G-protein-coupled receptors (GPCRs). The method discriminated amine subfamily of GPCRs from globular proteins with Matthew's correlation coefficient of 0.98 and 0.99 using amino acid composition and dipeptide composition, respectively. In classifying different types of amine receptors using amino acid composition and dipeptide composition, the method achieved an accuracy of 89.8 and 96.4%, respectively. The performance of the method was evaluated using 5-fold cross-validation. The dipeptide composition based method predicted 67.6% of protein sequences with an accuracy of 100% with a reliability index > or =5. A web server GPCRsclass has been developed for predicting amine-binding receptors from its amino acid sequence [http://www.imtech.res.in/raghava/gpcrsclass/ and http://bioinformatics.uams.edu/raghava/gpersclass/ (mirror site)].
Bhasin
Manoj
M
Bioinformatics Center, Institute of Microbial Technology, Sector 39A, Chandigarh, India.
Raghava
G P S
GP
D001185:Artificial Intelligence; D004151:Dipeptides / Q000737:chemistry; D020407:Internet; D011941:Receptors, Adrenergic / Q000737:chemistry / Q000145:classification; D017982:Receptors, Biogenic Amine / Q000737:chemistry / Q000145:classification*; D011950:Receptors, Cholinergic / Q000737:chemistry / Q000145:classification; D011954:Receptors, Dopamine / Q000737:chemistry / Q000145:classification; D043562:Receptors, G-Protein-Coupled / Q000737:chemistry / Q000145:classification*; D011985:Receptors, Serotonin / Q000737:chemistry / Q000145:classification; D020539:Sequence Analysis, Protein; D012984:Software
D004151:Dipeptides; D011941:Receptors, Adrenergic; D017982:Receptors, Biogenic Amine; D011950:Receptors, Cholinergic; D011954:Receptors, Dopamine; D043562:Receptors, G-Protein-Coupled; D011985:Receptors, Serotonin