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A Survey of Web-Based Chemogenomic Data Resources

  • Rasel Al Mahmud
  • Rifat Ara NajninEmail author
  • Ahsan Habib Polash
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1825)

Abstract

Chemogenomics is a comparatively nascent branch dealing with the effects of drugs and chemicals on molecular level systems. With the emergence of this new epoch, the quantity of data sources is also unprecedentedly increasing. Despite having a plethora of a databases, the variation in bioactivity measurement as well as bias toward specific protein studies, varied computational procedures and redundant information make data mining tedious, especially for newcomers in the field. In this chapter, we give an overview of hands-on data collection and domains of applicability from some useful Web-based chemogenomic resources that are accessible with nothing more than a Web browser. This overview can help assist users in acquiring chemogenomic datasets for their project at hand.

Key words

Chemogenomic resources World Wide Web Ligand-target data ChemProt STITCH PubChem ChEMBL ChEBI ChemSpider PharmGKB 

References

  1. 1.
    Neuman KC (2010) Single-molecule measurements of DNA topology and topoisomerases. J Biol Chem 285:18967–18971.  https://doi.org/10.1074/jbc.R109.092437CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Pommier Y, Sun Y, Huang SN, Nitiss JL (2016) Roles of eukaryotic topoisomerases in transcription, replication and genomic stability. Nat Rev Mol Cell Biol 17:703–721.  https://doi.org/10.1038/nrm.2016.111CrossRefPubMedGoogle Scholar
  3. 3.
    Kringelum J, Kjaerulff SK, Brunak S et al (2016) ChemProt-3.0: a global chemical biology diseases mapping. Database 2016:bav123.  https://doi.org/10.1093/database/bav123CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Szklarczyk D, Santos A, von Mering C et al (2015) STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Nucleic Acids Res 44:gkv1277.  https://doi.org/10.1093/nar/gkv1277CrossRefGoogle Scholar
  5. 5.
    Kuhn M, Szklarczyk D, Pletscher-Frankild S et al (2014) STITCH 4: integration of protein-chemical interactions with user data. Nucleic Acids Res 42:D401–D407.  https://doi.org/10.1093/nar/gkt1207CrossRefPubMedGoogle Scholar
  6. 6.
    Kim S, Thiessen PA, Bolton EE et al (2016) PubChem substance and compound databases. Nucleic Acids Res 44:D1202–D1213.  https://doi.org/10.1093/nar/gkv951CrossRefPubMedGoogle Scholar
  7. 7.
    Wang Y, Bryant SH, Cheng T et al (2017) PubChem BioAssay: 2017 update. Nucleic Acids Res 45:D955–D963.  https://doi.org/10.1093/nar/gkw1118CrossRefPubMedGoogle Scholar
  8. 8.
    Wang Y, Xiao J, Suzek TO et al (2012) PubChem’s BioAssay database. Nucleic Acids Res 40:D400–D412.  https://doi.org/10.1093/nar/gkr1132CrossRefPubMedGoogle Scholar
  9. 9.
    Gaulton A, Hersey A, Nowotka M et al (2017) The ChEMBL database in 2017. Nucleic Acids Res 45:D945–D954.  https://doi.org/10.1093/nar/gkw1074CrossRefPubMedGoogle Scholar
  10. 10.
    Gaulton A, Bellis LJ, Bento AP et al (2012) ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res 40:D1100–D1107.  https://doi.org/10.1093/nar/gkr777CrossRefPubMedGoogle Scholar
  11. 11.
    Bento AP, Gaulton A, Hersey A et al (2014) The ChEMBL bioactivity database: an update. Nucleic Acids Res 42:D1083–D1090.  https://doi.org/10.1093/nar/gkt1031CrossRefPubMedGoogle Scholar
  12. 12.
    Hastings J, de Matos P, Dekker A et al (2013) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res 41:D456–D463.  https://doi.org/10.1093/nar/gks1146CrossRefPubMedGoogle Scholar
  13. 13.
    Pence HE, Williams A (2010) ChemSpider: an online chemical information resource. J Chem Educ 87:1123–1124.  https://doi.org/10.1021/ed100697wCrossRefGoogle Scholar
  14. 14.
    Williams AJ, Tkachenko V, Golotvin S et al (2010) ChemSpider–building a foundation for the semantic web by hosting a crowd sourced databasing platform for chemistry. J Cheminform 2:O16.  https://doi.org/10.1186/1758-2946-2-S1-O16CrossRefPubMedCentralGoogle Scholar
  15. 15.
    Whirl-Carrillo M, McDonagh EM, Hebert JM et al (2012) Pharmacogenomics knowledge for personalized medicine. Clin Pharmacol Ther 92:414–417.  https://doi.org/10.1038/clpt.2012.96CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Hewett M, Oliver DE, Rubin DL et al (2002) PharmGKB: the pharmacogenetics knowledge base. Nucleic Acids Res 30:163–165CrossRefGoogle Scholar
  17. 17.
    Keiser MJ, Roth BL, Armbruster BN et al (2007) Relating protein pharmacology by ligand chemistry. Nat Biotechnol 25:197–206.  https://doi.org/10.1038/nbt1284CrossRefPubMedGoogle Scholar
  18. 18.
    Kanehisa M, Sato Y, Kawashima M et al (2016) KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 44:D457–D462.  https://doi.org/10.1093/nar/gkv1070CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Rasel Al Mahmud
    • 1
  • Rifat Ara Najnin
    • 1
    Email author
  • Ahsan Habib Polash
    • 1
  1. 1.Department of Radiation Genetics, Graduate School of MedicineKyoto UniversityKyotoJapan

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