GPCRRD: G protein-coupled receptor spatial restraint database for 3D structure modeling and function annotation

Bioinformatics

Volumn 26, Issue 23, 2010, Pages 3004-3005

  Zhang, Jian ^a   Zhang, Yang ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

G PROTEIN COUPLED RECEPTOR;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; MOLECULAR GENETICS; PHYSIOLOGY; PROTEIN DATABASE; PROTEIN MOTIF;

ALGORITHMS; AMINO ACID MOTIFS; DATABASES, PROTEIN; MODELS, MOLECULAR; MOLECULAR SEQUENCE ANNOTATION; RECEPTORS, G-PROTEIN-COUPLED;

EID: 78449294139     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq563     Document Type: Article

References (23)

1. Becker,O.M. et al. (2003) Modeling the 3D structure of GPCRs: advances and application to drug discovery. Curr. Opin. Drug Disc., 6, 353-361.
2. Beukers,M.W. et al. (1999) TinyGRAP database: a bioinformatics tool to mine G-protein-coupled receptor mutant data. Trends Pharmacol. Sci., 20, 475-477.
3. Du,P. et al. (1997) Modeling the G-protein-coupled neuropeptide YY1 receptor agonist and antagonist binding sites. Protein Eng., 10, 109-117.
4. Horn,F. et al. (2003) GPCRDB information system for G protein-coupled receptors. Nucleic Acids Res., 31, 294-297.
5. Jaakola,V.P. et al. (2008) The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist. Science, 322, 1211-1217.
6. Kanz,C. et al. (2005) The EMBL nucleotide sequence database. Nucleic Acids Res., 33, D29-D33.
7. Khelashvili,G. (2010) GPCR-OKB: the G protein coupled receptor oligomer knowledge base. Bioinformatics, 26, 1804-1805.
8. Krogh,A. et al. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol., 305, 567-580.
9. Michino,M. et al. (2009) Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nat. Rev. Drug Discov., 8, 455-463.
10. Moult,J. et al. (2009) Critical assessment of methods of protein structure prediction- Round VIII. Proteins, 77, 1-4.
11. Paiva,A.C.etal. (2006)Modeling GPCRs. Ernst Schering Found. Symp. Proc.,2,23-47.
12. Rosenbaum,D.M. et al. (2007) GPCR engineering yields high-resolution structural insights into beta2-adrenergic receptor function. Science, 318, 1266-1273.
13. Rosenbaum,D.M. et al. (2009) The structure and function of G-protein-coupled receptors. Nature, 459, 356-363.
14. Roy,A. et al. (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat. Protoc., 5, 725-738.
15. Sali,A. and Blundell,T.L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.
16. Schuler,G.D. et al. (1996) Entrez: Molecular biology database and retrieval system. Comput. Methods Macromol. Seq. Anal., 266, 141-162.
17. Schushan,M. et al. (2010) Cα-trace model of the transmembrane domain of human copper transporter 1, motion and functional implications. Proc. Natl Acad. Sci., 107, 10908-10913.
18. Shacham,S. et al. (2004) PREDICT modeling and in-silico screening for G-protein coupled receptors. Proteins, 57, 51-86.
19. Shi,L. and Javitch,J.A. (2002) The binding site of aminergic G protein-coupled receptors: The transmembrane segments and second extracellular loop. Annu. Rev. Pharmacol., 42, 437-467.
20. Skolnick,J. et al. (2000) Structural genomics and its importance for gene function analysis. Nat. Biotechnol., 18, 283-287.
21. Yip,Y.L. et al. (2008) Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase. Hum. Mutat., 29, 361-366.
22. Zhang,Y. et al. (2003) TOUCHSTONE II: A new approach to ab initio protein structure prediction. Biophys. J., 85, 1145-1164.
23. Zhang,Y. et al. (2006) Structure modeling of all identified G protein-coupled receptors in the human genome. PLoS Comput. Biol., 2, 88-99.