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How to Use the IUPHAR Receptor Database to Navigate Pharmacological Data

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Receptor Binding Techniques

Part of the book series: Methods in Molecular Biology ((MIMB,volume 897))

Abstract

Today’s data-intensive, interdisciplinary research challenges scientists to keep up to date with key experimental techniques and tools reported in the literature. The International Union of Basic and Clinical Pharmacology Database (IUPHAR-DB) goes some way to addressing this need by providing expert-curated information sourced from primary literature and displayed in a user-friendly manner online. The database provides a channel for the IUPHAR Nomenclature Committee (NC-IUPHAR) to provide recommendations on the nomenclature of receptors and ion channels, to document their properties and the ligands that are useful for receptor characterization. Here we describe IUPHAR-DB’s main features and provide examples of techniques for navigating and exploring the information. The database is freely available online at http://www.iuphar-db.org/.

The authors wish it to be known that the first two authors should be regarded as joint First Authors. NC-IUPHAR denotes International Union of Basic and Clinical Pharmacology Committee on Receptor Nomenclature and Drug Classification. The members of NC-IUPHAR are provided in Acknowledgement.

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References

  1. Harmar AJ, Hills RA, Rosser EM et al (2009) IUPHAR-DB: the IUPHAR database of G protein-coupled receptors and ion channels. Nucleic Acids Res 37:D680–D685

    Article  PubMed  CAS  Google Scholar 

  2. NC-IUPHAR.  http://www.iuphar-db.org/nciuphar.jsp. Accessed 12 April 2012

  3. Sharman JL, Mpamhanga CP, Spedding M et al (2011) IUPHAR-DB: new receptors and tools for easy searching and visualization of pharmacological data. Nucleic Acids Res 39:D534–D538

    Article  PubMed  Google Scholar 

  4. Hopkins AL, Groom CR (2002) The druggable genome. Nat Rev Drug Discov 1:727–730

    Article  PubMed  CAS  Google Scholar 

  5. Foord SM, Bonner TI, Neubig RR et al (2005) International union of pharmacology. XLVI. G protein-coupled receptor list. Pharmacol Rev 57:279–288

    Article  PubMed  CAS  Google Scholar 

  6. Germain P, Staels B, Dacquet C et al (2006) Overview of nomenclature of nuclear receptors. Pharmacol Rev 58:685–704

    Article  PubMed  CAS  Google Scholar 

  7. Collingridge GL, Olsen RW, Peters J et al (2009) A nomenclature for ligand-gated ion channels. Neuropharmacology 56:2–5

    Article  PubMed  CAS  Google Scholar 

  8. Yu FH, Yarov-Yarovoy V, Gutman GA et al (2005) Overview of molecular relationships in the voltage-gated ion channel superfamily. Pharmacol Rev 57:387–395

    Article  PubMed  CAS  Google Scholar 

  9. Seal RL, Gordon SM, Lush MJ et al (2011) genenames.org: the HGNC resources in 2011. Nucleic Acids Res 39:D514–D519

    Article  PubMed  Google Scholar 

  10. Blake JA, Bult CJ, Kadin JA et al (2011) The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. Nucleic Acids Res 39:D842–D848

    Article  PubMed  Google Scholar 

  11. Dwinell MR, Worthey EA, Shimoyama M et al (2009) The Rat Genome Database 2009: variation, ontologies and pathways. Nucleic Acids Res 37:D744–D749

    Article  PubMed  CAS  Google Scholar 

  12. Pruitt KD, Tatusova T, Klimke W et al (2009) NCBI reference sequences: current status, policy and new initiatives. Nucleic Acids Res 37:D32–D36

    Article  PubMed  CAS  Google Scholar 

  13. Maglott D, Ostell J, Pruitt KD et al (2011) Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 39:D52–D57

    Article  PubMed  Google Scholar 

  14. Amberger J, Bocchini CA, Scott AF et al (2009) McKusick’s Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res 37:D793–D796

    Article  PubMed  CAS  Google Scholar 

  15. UniProt_Consortium (2011) Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res 39:D214–D219

    Article  Google Scholar 

  16. Flicek P, Amode MR, Barrell D et al (2011) Ensembl 2011. Nucleic Acids Res 39:D800–D806

    Article  PubMed  Google Scholar 

  17. Safran M, Solomon I, Shmueli O et al (2002) GeneCards 2002: towards a complete, object-oriented, human gene compendium. Bioinformatics 18:1542–1543

    Article  PubMed  CAS  Google Scholar 

  18. Berman HM, Westbrook J, Feng Z et al (2000) The Protein Data Bank. Nucleic Acids Res 28:235–242

    Article  PubMed  CAS  Google Scholar 

  19. Wishart DS, Knox C, Guo AC et al (2008) DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res 36:D901–D906

    Article  PubMed  CAS  Google Scholar 

  20. Wang Y, Xiao J, Suzek TO et al (2009) PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res 37:W623–W633

    Article  PubMed  CAS  Google Scholar 

  21. Overington J (2009) ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI). Interview by Wendy A. Warr. J Comput Aided Mol Des 23:195–198

    Article  PubMed  Google Scholar 

  22. Steinbeck C, Hoppe C, Kuhn S et al (2006) Recent developments of the chemistry development kit (CDK)—an open-source java library for chemo- and bioinformatics. Curr Pharm Des 12:2111–2120

    Article  PubMed  CAS  Google Scholar 

  23. Lipinski CA, Lombardo F, Dominy BW et al (2001) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 46:3–26

    Article  PubMed  CAS  Google Scholar 

  24. PostgreSQL, version 9.0. http://www.postgresql.org. Accessed 30 March 2011

  25. PubMed.    http://www.ncbi.nlm.nih.gov/pubmed. Accessed 30 March 2011

  26. Andrade R, Barnes NM, Baxter G et al. 5-Hydroxytryptamine receptors. IUPHAR Database.      http://www.iuphar-db.org/DATABASE/FamilyMenuForward?familyId=1. Modified 28 Jan 2011. Accessed 30 March 2011

  27. Peters JA, Lummis SCR, Barnes NM et al. 5-HT3 receptors. IUPHAR Database. http://www.iuphar-db.org/DATABASE/FamilyMenuForward?familyId=68. Modified 7 Jan 2010. Accessed 30 March 2011

  28. Gutman GA, Aldrich R, Chandy KG et al. Calcium-activated potassium channels: KCa2.3. IUPHAR database. http://www.iuphar-db.org/DATABASE/ObjectDisplayForward?objectId=383. Modified 31 Jan 2011. Accessed 30 March 2011

  29. Pin JP, Neubig R, Bouvier M et al (2007) International union of basic and clinical pharmacology. LXVII. Recommendations for the recognition and nomenclature of G protein-coupled receptor heteromultimers. Pharmacol Rev 59:5–13

    Article  PubMed  CAS  Google Scholar 

  30. The Open Babel Package, version 2.2.3. http://openbabel.sourceforge.net/. Accessed 30 March 2011

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Acknowledgements

The authors thank all contributors and members of NC-IUPHAR and its subcommittees for their ongoing support. NC-IUPHAR members: S.P.H. Alexander, T.I. Bonner, W.A. Catterall, A. Christopoulos, A.P. Davenport, C.T. Dollery, S. Enna, A.J. Harmar, K. Kaibuchi, Y. Kanai, V. Laudet, R.R. Neubig, E.H. Ohlstein, J. Peters, J-P. Pin, U. Ruegg, P. du Souich, M. Spedding, and M.W. Wright. IUPHAR-DB has been developed with financial support from the British Pharmacological Society, ASPET, Servier, GlaxoSmithKline, Pfizer, Actelion, AstraZeneca, DiscoveRx, Lundbeck, Abbott, and Merck Millipore.

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Correspondence to Anthony J. Harmar .

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Mpamhanga, C.P., Sharman, J.L., Harmar, A.J., NC-IUPHAR. (2012). How to Use the IUPHAR Receptor Database to Navigate Pharmacological Data. In: Davenport, A. (eds) Receptor Binding Techniques. Methods in Molecular Biology, vol 897. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-909-9_2

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  • DOI: https://doi.org/10.1007/978-1-61779-909-9_2

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-908-2

  • Online ISBN: 978-1-61779-909-9

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