Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008
10.1038/nrd2877
Crossref journal-article
Springer Science and Business Media LLC
Nature Reviews Drug Discovery (297)
Bibliography

Michino, M., Abola, E., Brooks, C. L., Dixon, J. S., Moult, J., & Stevens, R. C. (2009). Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nature Reviews Drug Discovery, 8(6), 455–463.

Authors 7
  1. (first)
  2. Mayako Michino (first)
  3. Enrique Abola (additional)
  4. Charles L. Brooks (additional)
  5. J. Scott Dixon (additional)
  6. John Moult (additional)
  7. Raymond C. Stevens (additional)
References 37 Referenced 241
  1. Jorgensen, W. L. The many roles of computation in drug discovery. Science 303, 1813–1818 (2004). (10.1126/science.1096361) / Science by WL Jorgensen (2004)
  2. Richon, A. B. Current status and future direction of the molecular modeling industry. Drug Discov. Today 13, 665–669 (2008). (10.1016/j.drudis.2008.04.008) / Drug Discov. Today by AB Richon (2008)
  3. Kitchen, D. B., Decornez, H., Furr, J. R. & Bajorath, J. Docking and scoring in virtual screening for drug discovery: methods and applications. Nature Rev. Drug Discov. 3, 935–949 (2004). (10.1038/nrd1549) / Nature Rev. Drug Discov. by DB Kitchen (2004)
  4. Drews, J. Drug discovery: a historical perspective. Science 287, 1960–1964 (2000). (10.1126/science.287.5460.1960) / Science by J Drews (2000)
  5. Klabunde, T. & Hessler, G. Drug design strategies for targeting G-protein-coupled receptors. Chembiochem. 3, 928–944 (2002). (10.1002/1439-7633(20021004)3:10<928::AID-CBIC928>3.0.CO;2-5) / Chembiochem. by T Klabunde (2002)
  6. Becker, O. M. et al. G protein-coupled receptors: in silico drug discovery in 3D. Proc. Natl Acad. Sci. USA 101, 11304–11309 (2004). (10.1073/pnas.0401862101) / Proc. Natl Acad. Sci. USA by OM Becker (2004)
  7. Ballesteros, J. & Palczewski, K. G protein-coupled receptor drug discovery: implications from the crystal structure of rhodopsin. Curr. Opin. Drug Discov. Devel. 4, 561–574 (2001). / Curr. Opin. Drug Discov. Devel. by J Ballesteros (2001)
  8. Bu, L., Michino, M., Wolf, R. M. & Brooks, C. L. III. Improved model building and assessment of the Calcium-sensing receptor transmembrane domain. Proteins 71, 215–226 (2008). (10.1002/prot.21685) / Proteins by L Bu (2008)
  9. Henin, J. et al. Probing a model of a GPCR/ligand complex in an explicit membrane environment: the human cholecystokinin-1 receptor. Biophys. J. 90, 1232–1240 (2006). (10.1529/biophysj.105.070599) / Biophys. J. by J Henin (2006)
  10. Fowler, C. B., Pogozheva, I. D., LeVine, H., 3rd & Mosberg, H. I. Refinement of a homology model of the mu-opioid receptor using distance constraints from intrinsic and engineered zinc-binding sites. Biochemistry 43, 8700–8710 (2004). (10.1021/bi036067r) / Biochemistry by CB Fowler (2004)
  11. Evers, A. & Klabunde, T. Structure-based drug discovery using GPCR homology modeling: successful virtual screening for antagonists of the alpha1A adrenergic receptor. J. Med. Chem. 48, 1088–1097 (2005). (10.1021/jm0491804) / J. Med. Chem. by A Evers (2005)
  12. Manivet, P. et al. The serotonin binding site of human and murine 5-HT2B receptors: molecular modeling and site-directed mutagenesis. J. Biol. Chem. 277, 17170–17178 (2002). (10.1074/jbc.M200195200) / J. Biol. Chem. by P Manivet (2002)
  13. Archer, E., Maigret, B., Escrieut, C., Pradayrol, L. & Fourmy, D. Rhodopsin crystal: new template yielding realistic models of G-protein-coupled receptors? Trends Pharmacol. Sci. 24, 36–40 (2003). (10.1016/S0165-6147(02)00009-3) / Trends Pharmacol. Sci. by E Archer (2003)
  14. Gershengorn, M. C. & Osman, R. Minireview: Insights into G protein-coupled receptor function using molecular models. Endocrinology 142, 2–10 (2001). (10.1210/endo.142.1.7919) / Endocrinology by MC Gershengorn (2001)
  15. Ballesteros, J. A., Shi, L. & Javitch, J. A. Structural mimicry in G protein-coupled receptors: implications of the high-resolution structure of rhodopsin for structure-function analysis of rhodopsin-like receptors. Mol. Pharmacol. 60, 1–19 (2001). (10.1124/mol.60.1.1) / Mol. Pharmacol. by JA Ballesteros (2001)
  16. Kobilka, B. K. & Deupi, X. Conformational complexity of G-protein-coupled receptors. Trends Pharmacol. Sci. 28, 397–406 (2007). (10.1016/j.tips.2007.06.003) / Trends Pharmacol. Sci. by BK Kobilka (2007)
  17. Bhattacharya, S., Hall, S. E., Li, H. & Vaidehi, N. Ligand-stabilized conformational states of human beta(2) adrenergic receptor: insight into G-protein-coupled receptor activation. Biophys. J. 94, 2027–2042 (2008). (10.1529/biophysj.107.117648) / Biophys. J. by S Bhattacharya (2008)
  18. Kenakin, T. Efficacy at G-protein-coupled receptors. Nature Rev. Drug Discov. 1, 103–110 (2002). (10.1038/nrd722) / Nature Rev. Drug Discov. by T Kenakin (2002)
  19. Jaakola, V. P. et al. The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist. Science 322, 1211–1217 (2008). The human adenosine A 2A receptor crystal structure served as the experimental template for comparison for this modelling and docking assessment. This is the second human GPCR structure to be experimentally determined. (10.1126/science.1164772) / Science by VP Jaakola (2008)
  20. Jacobson, K. A. & Gao, Z. G. Adenosine receptors as therapeutic targets. Nature Rev. Drug Discov. 5, 247–264 (2006). (10.1038/nrd1983) / Nature Rev. Drug Discov. by KA Jacobson (2006)
  21. Moult, J. et al. Critical assessment of methods of protein structure prediction-Round VII. Proteins 69 (Suppl. 8), 3–9 (2007). The very successful CASP (Critical Assessment of Protein Structure) project started in 1994 and served as the model to conduct the reported GPCR Dock 2008 modelling and docking assessment. (10.1002/prot.21767) / Proteins by J Moult (2007)
  22. Lensink, M. F., Mendez, R. & Wodak, S. J. Docking and scoring protein complexes: CAPRI 3rd Edition. Proteins 69, 704–718 (2007). (10.1002/prot.21804) / Proteins by MF Lensink (2007)
  23. Kopp, J., Bordoli, L., Battey, J. N., Kiefer, F. & Schwede, T. Assessment of CASP7 predictions for template-based modeling targets. Proteins 69 (Suppl. 8), 38–56 (2007). (10.1002/prot.21753) / Proteins by J Kopp (2007)
  24. Kobilka, B. & Schertler, G. F. New G-protein-coupled receptor crystal structures: insights and limitations. Trends Pharmacol. Sci. 29, 79–83 (2008). (10.1016/j.tips.2007.11.009) / Trends Pharmacol. Sci. by B Kobilka (2008)
  25. Jacobson, M. P. et al. A hierarchical approach to all-atom protein loop prediction. Proteins 55, 351–367 (2004). (10.1002/prot.10613) / Proteins by MP Jacobson (2004)
  26. Rohl, C. A., Strauss, C. E., Chivian, D. & Baker, D. Modeling structurally variable regions in homologous proteins with rosetta. Proteins 55, 656–677 (2004). (10.1002/prot.10629) / Proteins by CA Rohl (2004)
  27. Friesner, R. A. et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 47, 1739–1749 (2004). (10.1021/jm0306430) / J. Med. Chem. by RA Friesner (2004)
  28. Totrov, M. & Abagyan, R. Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins 29 (Suppl. 1), 215–220 (1997). (10.1002/(SICI)1097-0134(1997)1+<215::AID-PROT29>3.0.CO;2-Q) / Proteins by M Totrov (1997)
  29. Verdonk, M. L., Cole, J. C., Hartshorn, M. J., Murray, C. W. & Taylor, R. D. Improved protein-ligand docking using GOLD. Proteins 52, 609–623 (2003). (10.1002/prot.10465) / Proteins by ML Verdonk (2003)
  30. Morris, G. et al. Automated docking using a lamarkian genetic algorithm and empirical binding free energy function. J. Comput. Chem. 19, 1639–1662 (1998). (10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B) / J. Comput. Chem. by G Morris (1998)
  31. Mirzadegan, T., Benko, G., Filipek, S. & Palczewski, K. Sequence analyses of G-protein-coupled receptors: similarities to rhodopsin. Biochemistry 42, 2759–2767 (2003). (10.1021/bi027224+) / Biochemistry by T Mirzadegan (2003)
  32. Baker, D. & Sali, A. Protein structure prediction and structural genomics. Science 294, 93–96 (2001). The use of protein models and docking is dependent on how such data will be used. In this paper, Baker and Sali provide an excellent presentation of where models are useful, in particular as hypothesis generators with the application being dependent on the resolution of the structure. (10.1126/science.1065659) / Science by D Baker (2001)
  33. Fredriksson, R., Lagerstrom, M. C., Lundin, L. G. & Schioth, H. B. The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints. Mol. Pharmacol. 63, 1256–1272 (2003). (10.1124/mol.63.6.1256) / Mol. Pharmacol. by R Fredriksson (2003)
  34. Marti-Renom, M. A. et al. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291–325 (2000). (10.1146/annurev.biophys.29.1.291) / Annu. Rev. Biophys. Biomol. Struct. by MA Marti-Renom (2000)
  35. Read, R. J. & Chavali, G. Assessment of CASP7 predictions in the high accuracy template-based modeling category. Proteins 69 (Suppl. 8), 27–37 (2007). (10.1002/prot.21662) / Proteins by RJ Read (2007)
  36. Kim, J. et al. Glutamate residues in the second extracellular loop of the human A2a adenosine receptor are required for ligand recognition. Mol. Pharmacol. 49, 683–691 (1996). (10.1016/S0026-895X(25)08783-8) / Mol. Pharmacol. by J Kim (1996)
  37. Barth, P., Schonbrun, J. & Baker, D. Toward high-resolution prediction and design of transmembrane helical protein structures. Proc. Natl Acad. Sci. USA 104, 15682–15687 (2007). (10.1073/pnas.0702515104) / Proc. Natl Acad. Sci. USA by P Barth (2007)
Dates
Type When
Created 16 years, 2 months ago (June 16, 2009, 9:37 a.m.)
Deposited 6 months, 2 weeks ago (Feb. 9, 2025, 11:52 p.m.)
Indexed 1 month, 3 weeks ago (July 3, 2025, 2:28 a.m.)
Issued 16 years, 3 months ago (May 22, 2009)
Published 16 years, 3 months ago (May 22, 2009)
Published Online 16 years, 3 months ago (May 22, 2009)
Published Print 16 years, 2 months ago (June 1, 2009)
Funders 0

None

@article{2009, title={Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008}, volume={8}, ISSN={1474-1784}, url={http://dx.doi.org/10.1038/nrd2877}, DOI={10.1038/nrd2877}, number={6}, journal={Nature Reviews Drug Discovery}, publisher={Springer Science and Business Media LLC}, author={Michino, Mayako and Abola, Enrique and Brooks, Charles L. and Dixon, J. Scott and Moult, John and Stevens, Raymond C.}, year={2009}, month=may, pages={455–463} }