Erratum: GPCRdb: An information system for G protein-coupled receptors (Nucleic Acids Research (2016) 44 (D356-D364) DOI: 10.1093/nar/gkv1178);GPCRdb: An information system for G protein-coupled receptors

Nucleic Acids Research

Volumn 44, Issue D1, 2016, Pages D356-D364

  Isberg, Vignir ^a   Mordalski, Stefan ^b   Munk, Christian ^a   Rataj, Krzysztof ^b   Harpsøe, Kasper ^a   Hauser, Alexander S ^a   Vroling, Bas ^c   Bojarski, Andrzej J ^b   Vriend, Gert ^d   Gloriam, David E ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b INSTITUTE OF PHARMACOLOGY   (Poland)

^c Bio Prodict   (Netherlands)

^d RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

G PROTEIN COUPLED RECEPTOR; LIGAND;

ARTICLE; CRYSTAL STRUCTURE; HYDROGEN BOND; INFORMATION SYSTEM; LIGAND BINDING; PHYLOGENETIC TREE; POINT MUTATION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DATABASE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; BINDING SITE; CHEMISTRY; CLASSIFICATION; GENETICS; HUMAN; METABOLISM; MUTATION; PHYLOGENY; SOFTWARE;

BINDING SITES; DATABASES, PROTEIN; HUMANS; LIGANDS; MUTATION; PHYLOGENY; RECEPTORS, G-PROTEIN-COUPLED; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 84976904319     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw1218     Document Type: Erratum

References (49)

1. Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A. et al. (2001) The sequence of the human genome. Science, 291, 1304-1351.
2. Mombaerts, P. (2004) Genes and ligands for odorant, vomeronasal and taste receptors. Nat. Rev. Neurosci., 5, 263-278.
3. Kolakowski, L. F. Jr (1994) GCRDb: a G-protein-coupled receptor database. Receptors Channels, 2, 1-7.
4. Fredriksson, R., Lagerström, M. C., Lundin, L.-G. and Schiöth, H. B. (2003) The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints. Mol. Pharmacol., 63, 1256-1272.
5. Southan, C., Sharman, J. L., Benson, H. E., Faccenda, E., Pawson, A. J., Alexander, S. P. H., Buneman, O. P., Davenport, A. P., McGrath, J. C., Peters, J. A. et al. (2015) The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towardscurated quantitative interactions between 1300 protein targets and 6000 ligands. Nucleic Acids Res., doi:10.1093/nar/gkv1037.
6. Overington, J. P., Al-Lazikani, B. and Hopkins, A. L. (2006) How many drug targets are there? Nat. Rev. Drug Discov., 5, 993-996.
7. Rask-Andersen, M., Masuram, S. and Schioth, H. B. (2014) The druggable genome: evaluation of drug targets in clinical trials suggests major shifts in molecular class and indication. Annu. Rev. Pharmacol. Toxicol., 54, 9-26.
8. Kenakin, T. (2013) New concepts in pharmacological efficacy at 7TM receptors: IUPHAR Review 2. Br. J. Pharmacol., 168, 554-575.
9. Kruse, A. C., Ring, A. M., Manglik, A., Hu, J., Hu, K., Eitel, K., Hubner, H., Pardon, E., Valant, C., Sexton, P. M. et al. (2013) Activation and allosteric modulation of a muscarinic acetylcholine receptor. Nature, 504, 101-106.
10. Venkatakrishnan, A. J., Deupi, X., Lebon, G., Tate, C. G., Schertler, G. F. and Babu, M. M. (2013) Molecular signatures of G-protein-coupled receptors. Nature, 494, 185-194.
11. Tehan, B. G., Bortolato, A., Blaney, F. E., Weir, M. P. and Mason, J. S. (2014) Unifying family A GPCR theories of activation. Pharmacol. Ther., 143, 51-60.
12. Katritch, V., Cherezov, V. and Stevens, R. C. (2013) Structure-function of the G protein-coupled receptor superfamily. Annu. Rev. Pharmacol. Toxicol., 53, 531-556.
13. Rasmussen, S. G., DeVree, B. T., Zou, Y., Kruse, A. C., Chung, K. Y., Kobilka, T. S., Thian, F. S., Chae, P. S., Pardon, E., Calinski, D. et al. (2011) Crystal structure of the beta2 adrenergic receptor-Gs protein complex. Nature, 477, 549-555.
14. Scheerer, P., Park, J. H., Hildebrand, P. W., Kim, Y. J., Krauss, N., Choe, H.-W., Hofmann, K. P. and Ernst, O. P. (2008) Crystal structure of opsin in its G-protein-interacting conformation. Nature, 455, 497-502.
15. Kang, Y., Zhou, X. E., Gao, X., He, Y., Liu, W., Ishchenko, A., Barty, A., White, T. A., Yefanov, O., Han, G. W. et al. (2015) Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser. Nature, 523, 561-567.
16. Lagerstrom, M. C. and Schioth, H. B. (2008) Structural diversity of G protein-coupled receptors and significance for drug discovery. Nat. Rev. Drug Discov., 7, 339-357.
17. Vroling, B., Sanders, M., Baakman, C., Borrmann, A., Verhoeven, S., Klomp, J., Oliveira, L., de Vlieg, J. and Vriend, G. (2011) GPCRDB: information system for G protein-coupled receptors. Nucleic Acids Res., 39, 309-319.
18. Horn, F., Bettler, E., Oliveira, L., Campagne, F., Cohen, F. E. and Vriend, G. (2003) GPCRDB information system for G protein-coupled receptors. Nucleic Acids Res., 31, 294-297.
19. Horn, F., Vriend, G. and Cohen, F. E. (2001) Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems. Nucleic Acids Res., 29, 346-349.
20. Horn, F., Weare, J., Beukers, M. W., Horsch, S., Bairoch, A., Chen, W., Edvardsen, O., Campagne, F. and Vriend, G. (1998) GPCRDB: an information system for G protein-coupled receptors. Nucleic Acids Res., 26, 275-279.
21. Isberg, V., Vroling, B., van der Kant, R., Li, K., Vriend, G. and Gloriam, D. (2014) GPCRDB: an information system for G protein-coupled receptors. Nucleic Acids Res., 42, D422-D425.
22. The UniProt Consortium. (2015) UniProt: a hub for protein information. Nucleic Acids Res., 43, D204-D212.
23. Davenport, A. P., Alexander, S. P., Sharman, J. L., Pawson, A. J., Benson, H. E., Monaghan, A. E., Liew, W. C., Mpamhanga, C. P., Bonner, T. I., Neubig, R. R. et al. (2013) International Union of Basic and Clinical Pharmacology. LXXXVIII. G protein-coupled receptor list: recommendations for new pairings with cognate ligands. Pharmacol. Rev., 65, 967-986.
24. Isberg, V., de Graaf, C., Bortolato, A., Cherezov, V., Katritch, V., Marshall, F. H., Mordalski, S., Pin, J., Stevens, R. C., Vriend, G. et al. (2015) Generic GPCR residue numbers - aligning topology maps while minding the gaps. Trends Pharmacol. Sci., 36, 22-31.
25. Rose, P. W., Prlic, A., Bi, C., Bluhm, W. F., Christie, C. H., Dutta, S., Green, R. K., Goodsell, D. S., Westbrook, J. D., Woo, J., Young, J., Zardecki, C., Berman, H. M., Bourne, P. E. and Burley, S. K. (2015) The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Res., 43, D345-D356.
26. Kuipers, R. K., Joosten, H. J., van Berkel, W. J., Leferink, N. G., Rooijen, E., Ittmann, E., van Zimmeren, F., Jochens, H., Bornscheuer, U., Vriend, G. et al. (2010) 3DM: systematic analysis of heterogeneous superfamily data to discover protein functionalities. Proteins, 78, 2101-2113.
27. Johnson, M., Zaretskaya, I., Raytselis, Y., Merezhuk, Y., McGinnis, S. and Madden, T. L. (2008) NCBI BLAST: a better web interface. Nucleic Acids Res., 36, W5-W9.
28. Felsenstein, J. (1989) PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics, 5, 164-166.
29. Beukers, M. W., Kristiansen, K., Ijzerman, A. P. and Edvardsen, O. (1999) TinyGRAP database: a bioinformatics tool to mine G-protein-coupled receptor mutant data. Trends Pharmacol. Sci., 20, 475-477.
30. Stierand, K. and Rarey, M. (2010) Drawing the PDB: protein-ligand complexes in two dimensions. ACS Med. Chem. Lett., 1, 540-545.
31. Fidom, K., Isberg, V., Hauser, A. S., Mordalski, S., Lehto, T., Bojarski, A. J. and Gloriam, D. E. (2015) A new crystal structure fragment-based pharmacophore method for G protein-coupled receptors. Methods, 71, 104-112.
32. Gloriam, D. E., Foord, S. M., Blaney, F. E. and Garland, S. L. (2009) Definition of the G protein-coupled receptor transmembrane bundle binding pocket and calculation of receptor similarities for drug design. J. Med. Chem., 52, 4429-4442.
33. Ballesteros, J. A. and Weinstein, H. (1995) Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors. Methods Neurosci., 25, 366-428.
34. Wootten, D., Simms, J., Miller, L. J., Christopoulos, A. and Sexton, P. M. (2013) Polar transmembrane interactions drive formation of ligand-specific and signal pathway-biased family B G protein-coupled receptor conformations. Proc. Natl. Acad. Sci. U. S. A., 110, 5211-5216.
35. Pin, J. P., Galvez, T. and Prezeau, L. (2003) Evolution, structure, and activation mechanism of family 3/C G-protein-coupled receptors. Pharmacol. Ther., 98, 325-354.
36. Wang, C., Wu, H., Evron, T., Vardy, E., Han, G., Huang, X., Hufeisen, S., Mangano, T., Urban, D., Katritch, V., Cherezov, V., Caron, M. G., Roth, B. L. and Stevens, R. C. (2014) Structural basis for smoothened receptor modulation and chemoresistance. Nat. Commun., 5, 4355.
37. Wiener, A., Shudler, M., Levit, A. and Niv, M. Y. (2012) BitterDB: a database of bitter compounds. Nucleic Acids Res., 40, D413-D419.
38. Latek, D., Pasznik, P., Carlomagno, T. and Filipek, S. (2013) Towards improved quality of GPCR models by usage of multiple templates and profile-profile comparison. PLoS One, 8, e56742.
39. Sandal, M., Duy, T. P., Cona, M., Zung, H., Carloni, P., Musiani, F. and Giorgetti, A. (2013) GOMoDo: a GPCRs online modeling and docking webserver. PLoS One, 8, e74092.
40. Worth, C., Kreuchwig, A., Kleinau, G. and Krause, G. (2011) GPCR-SSFE: a comprehensive database of G-protein-coupled receptor template predictions and homology models. BMC Bioinformatics, 12, 185.
41. Rodríguez, D., Bello, X. and Gutiérrez-de-Terán, H. (2012) Molecular modelling of G protein-coupled receptors through the web. Mol. Inform., 31, 334-341.
42. Michino, M., Abola, E., Brooks, C. L. 3rd, Dixon, J. S., Moult, J. and Stevens, R. C. (2009) Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nat. Rev. Drug Discov., 8, 455-463.
43. Kufareva, I., Rueda, M., Katritch, V., Stevens, R. C. and Abagyan, R. (2011) Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure, 19, 1108-1126.
44. Kufareva, I., Katritch, V. and Participants of, G. D. Participants of, G. D., Stevens, R. C. and Abagyan, R. (2014) Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges. Structure, 22, 1120-1139.
45. Harpsoe, K., Isberg, V., Tehan, B. G., Weiss, D., Arsova, A., Marshall, F. H., Brauner-Osborne, H. and Gloriam, D. E. (2015) Selective negative allosteric modulation of metabotropic glutamate receptors - a structural perspective of ligands and mutants. Sci. Rep., 5, 13869.
46. Wu, B., Chien, E. Y. T., Mol, C. D., Fenalti, G., Liu, W., Katritch, V., Abagyan, R., Brooun, A., Wells, P., Bi, F. C. et al. (2010) Structures of the CXCR4 Chemokine GPCR with small-molecule and cyclic peptide antagonists. Science, 330, 1066-1071.
47. Manglik, A., Kruse, A. C., Kobilka, T. S., Thian, F. S., Mathiesen, J. M., Sunahara, R. K., Pardo, L., Weis, W. I., Kobilka, B. K. and Granier, S. (2012) Crystal structure of the micro-opioid receptor bound to a morphinan antagonist. Nature, 485, 321-326.
48. Wu, H., Wacker, D., Mileni, M., Katritch, V., Han, G. W., Vardy, E., Liu, W., Thompson, A. A., Huang, X. P., Carroll, F. I. et al. (2012) Structure of the human kappa-opioid receptor in complex with JDTic. Nature, 485, 327-332.
49. Huang, J., Chen, S., Zhang, J. J. and Huang, X. Y. (2013) Crystal structure of oligomeric beta1-adrenergic G protein-coupled receptors in ligand-free basal state. Nat. Struct. Mol. Biol., 20, 419-425.