Bioinformatics approaches for the classification of G-protein-coupled receptors

Current Opinion in Pharmacology

Volumn 3, Issue 2, 2003, Pages 114-120

  Gaulton, Anna ^a   Attwood, Teresa K ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

G PROTEIN COUPLED RECEPTOR; LIGAND;

AMINO ACID SEQUENCE; BIOINFORMATICS; CLASSIFICATION; DRUG RECEPTOR BINDING; DRUG TARGETING; ENZYME SPECIFICITY; HUMAN; HUMAN GENOME; LIGAND BINDING; PRESCRIPTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN STRUCTURE; REVIEW; SEQUENCE ALIGNMENT; SEQUENCE DATABASE;

ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GTP-BINDING PROTEINS; HUMANS; RECEPTORS, CELL SURFACE;

EID: 0037385599     PISSN: 14714892     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1471-4892(03)00005-5     Document Type: Review

References (32)

1. Takeda S, Kadowaki S, Haga S, Takaesu H, Mitaku S: Identification of G-protein-coupled receptor genes from the human genome sequence. FEBS Lett 2002, 520:97-101.
2. Foord SM: Receptor classification: post genome. Curr Opin Pharmacol 2002, 2:561-566.
3. Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Le Trong I, Teller DC, Okada T, Stenkamp RE et al.: Crystal structure of rhodopsin: a G-protein-coupled receptor. Science 2000, 289:739-745.
4. Altschul SF, Gish W, Miller W: Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
5. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
6. Pearson WR, Lipman DJ: Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988, 85:2444-2448.
7. Pearson WR: Flexible sequence similarity searching with the FASTA3 program package. Methods Mol Biol 2000, 132:185-219.
8. Lee DK, Nguyen T, Lynch KR, Cheng R, Vanti WB, Arkhitko O, Lewis T, Evans JF, George SR, O'Dowd BF: Discovery and mapping of ten novel G-protein-coupled receptor genes. Gene 2001, 275:83-91.
9. Radford JC, Davies SA, Dow JA: Systematic G-protein-coupled receptor analysis in Drosophila melanogaster identifies a leucokinin receptor with novel roles. J Biol Chem 2002, 277:38810-38817.
10. Hewes RS, Taghert PH: Neuropeptides and neuropeptide receptors in the Drosophila melanogaster genome. Genome Res 2001, 11:1126-1142.
11. Zozulya S, Echeverri F, Nguyen T: The human olfactory receptor repertoire. Genome Biol 2001, 2:research0018.1-0018.12.
12. Falquet L, Pagni M, Bucher P, Hulo N, Sigrist CJ, Hofmann K, Bairoch A: The PROSITE database, its status in 2002. Nucleic Acids Res 2002, 30:235-238.
13. Huang JY, Brutlag DL: The EMOTIF database. Nucleic Acids Res 2001, 29:202-204.
14. Attwood TK, Blythe MJ, Flower DR, Gaulton A,Mabey JE, Maudling N, McGregor L, Mitchell AL, Moulton G, Paine K, Scordis P: PRINTS and PRINTS-S shed light on protein ancestry. Nucleic Acids Res 2002, 30:239-241.
15. Henikoff JG, Greene EA, Pietrokovski S, Henikoff S: Increased coverage of protein families with the blocks database servers. Nucleic Acids Res 2000, 28:228-230.
16. Gribskov M, McLachlan AD, Eisenberg D: Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci USA 1987, 84:4355-4358.
17. Bucher P, Bairoch A: A generalized profile syntax for biomolecular sequence motifs and its function in automatic sequence interpretation. Proc Int Conf Intell Syst Mol Biol 1994, 2:53-61.
18. Krogh A, Brown M, Mian IS, Sjolander K, Haussler D: Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol 1994, 235:1501-1531.
19. Eddy SR: Profile hidden Markov models. Bioinformatics 1998, 14:755-763.
20. The ISREC ProfileScan server. URL: http://hits.isb-sib.ch/cgi-bin/PFSCAN.
21. Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL: The Pfam protein families database. Nucleic Acids Res 2002, 30:276-280.
22. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P et al.: InterPro: an integrated documentation resource for protein families, domains and functional sites. Brief Bioinform 2002, 3:225-235.
23. Brody T, Cravchik A: Drosophila melanogaster G-protein-coupled receptors. J Cell Biol 2000, 150:F83-F88.
24. Remm M, Sonnhammer E: Classification of transmembrane protein families in the Caenorhabditis elegans genome and identification of human orthologs. Genome Res 2000, 10:1679-1689.
25. Attwood TK, Croning MD, Gaulton A: Deriving structural and functional insights from a ligand-based hierarchical classification of G-protein-coupled receptors. Protein Eng 2002, 15:7-12.
26. Joost P, Methner A: Phylogenetic analysis of 277 human G-protein-coupled receptors as a tool for the prediction of orphan receptor ligands. Genome Biol 2002, 3:research0063.1-0063.16.
27. Karchin R, Karplus K, Haussler D: Classifying G-protein-coupled receptors with support vector machines. Bioinformatics 2002, 18:147-159.
28. Lapinsh M, Gutcaits A, Prusis P, Post C, Lundstedt T, Wikberg JES: Classification of G-protein-coupled receptors by alignment-independent extraction of principal chemical properties of primary amino acid sequences. Protein Sci 2002, 11:795-805.
29. Parrill AL, Wang D, Bautista DL, Van Brocklyn JR, Lorincz Z, Fischer DJ, Baker DL, Liliom K, Spiegel S, Tigyi G: Identification of Edg1 receptor residues that recognize sphingosine 1-phosphate. J Biol Chem 2000, 275:39379-39384.
30. 1 (EDG2) phospholipid growth factor receptors. J Biol Chem 2001, 276:49213-49220.
31. Vaidehi N, Floriano WB, Trabanino R, Hall SE, Freddolino P, Choi EJ, Zamanakos G, Goddard WA III: Prediction of structure and function of G-protein-coupled receptors. Proc Natl Acad Sci USA 2002, 99:12622-12627.
32. Scordis P, Flower DR, Attwood TK: FingerPRINTScan: intelligent searching of the PRINTS motif database. Bioinformatics 1999, 15:523-524.