Skip to main content

Advertisement

Springer Nature Link
Log in

Tautomerism in chemical information management systems

  • Published:
Journal of Computer-Aided Molecular Design Aims and scope Submit manuscript

Abstract

Tautomerism has an impact on many of the processes in chemical information management systems including novelty checking during registration into chemical structure databases; storage of structures; exact and substructure searching in chemical structure databases; and depiction of structures retrieved by a search. The approaches taken by 27 different software vendors and database producers are compared. It is hoped that this comparison will act as a discussion document that could ultimately improve databases and software for researchers in the future.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10
Fig. 11
Fig. 12
Fig. 13
Fig. 14
Fig. 15
Fig. 16
Fig. 17
Fig. 18
Fig. 19
Fig. 20
Fig. 21
Fig. 22
Fig. 23

Similar content being viewed by others

References

  1. Warr WA (1999). Balancing the needs of the recruiters and the aims of the educators. Book of Abstracts, 218th ACS National Meeting, New Orleans, Aug. 22-26, 1999: COMP

  2. Warr WA Extract from 218th ACS National Meeting and Exposition New Orleans, Louisiana, August 22-26, 1999. http://warr.com/warrzone2000.html. Accessed 28 Feb 2010

  3. Morgan HL (1965) J Chem Doc 5(2):107

    Article  CAS  Google Scholar 

  4. Dittmar PG, Stobaugh RE, Watson CE (1976) J Chem Inf Comput Sci 16(2):111

    CAS  Google Scholar 

  5. Freeland RG, Funk SA, O’Korn LJ, Wilson GA (1979) J Chem Inf Comput Sci 19(2):94

    CAS  Google Scholar 

  6. Blackwood JE, Elliott PM, Stobaugh RE, Watson CE (1977) J Chem Inf Comput Sci 17(1):3

    CAS  Google Scholar 

  7. Vander Stouw GG, Gustafson C, Rule JD, Watson CE (1976) J Chem Inf Comput Sci 16(4):213

    CAS  Google Scholar 

  8. Zamora A, Dayton DL (1976) J Chem Inf Comput Sci 16(4):219

    CAS  Google Scholar 

  9. Stobaugh RE (1980) J Chem Inf Comput Sci 20(2):76

    CAS  Google Scholar 

  10. Mockus J, Stobaugh RE (1980) J Chem Inf Comput Sci 20(1):18

    CAS  Google Scholar 

  11. Moosemiller JP, Ryan AW, Stobaugh RE (1980) J Chem Inf Comput Sci 20(2):83

    CAS  Google Scholar 

  12. Ryan AW, Stobaugh RE (1982) J Chem Inf Comput Sci 22(1):22

    CAS  Google Scholar 

  13. Hamill KA, Nelson RD, Vander Stouw GG, Stobaugh RE (1988) J Chem Inf Comput Sci 28(4):175

    CAS  Google Scholar 

  14. Stobaugh RE (1988) J Chem Inf Comput Sci 28(4):180

    CAS  Google Scholar 

  15. Blackwood JE, Blower PE Jr, Layten SW, Lillie DH, Lipkus AH, Peer JP, Qian C, Staggenborg LM, Watson CE (1991) J Chem Inf Comput Sci 31(2):204

    CAS  Google Scholar 

  16. CTfile formats. http://www.symyx.com/downloads/public/ctfile/ctfile.jsp. Accessed 28 Feb 2010

  17. Dalby A, Nourse JG, Hounshell WD, Gushurst AKI, Grier DL, Leland BA, Laufer J (1992) J Chem Inf Comput Sci 32(3):244

    CAS  Google Scholar 

  18. The IUPAC International Chemical Identifier (InChI). http://www.iupac.org/inchi/. Accessed 28 Feb 2010

  19. Weininger D (1988) J Chem Inf Comput Sci 28(1):31

    CAS  Google Scholar 

  20. Weininger D, Weininger A, Weininger JL (1989) J Chem Inf Comput Sci 29(2):97

    CAS  Google Scholar 

  21. Wipke WT, Dyott TM (1974) J Am Chem Soc 96(15):4834

    Article  CAS  Google Scholar 

  22. NEMA key based exact match searching. http://www.symyx.com/solutions/white_papers/nema_whitepaper.jsp. Accessed 28 Feb 2010

  23. Wipke WT, Krishnan S, Ouchi GI (1978) J Chem Inf Comput Sci 18(1):32

    CAS  Google Scholar 

  24. Heller SR, McNaught AD (2009) Chem Int 31(1):7

    CAS  Google Scholar 

  25. InChI Technical Manual. http://www.iupac.org/inchi/download/index.html. Accessed 28 Feb 2010 (The file InChI_TechMan is included in stdinchi-1-doc.zip, inside the folder DOC-101)

  26. Secure hash standard. http://csrc.nist.gov/publications/fips/fips180-2/fips180-2withchangenotice.pdf. Accessed 28 Feb 2010

  27. The National Cancer Institute Computer-Aided Drug Design Group Chemical Structure Lookup Service (CSLS). http://cactus.nci.nih.gov/lookup. Accessed 28 Feb 2010

  28. Sitzmann M, Ihlenfeldt W-D, Nicklaus MC (2010) J Comput-Aided Mol Des. doi:10.1007/s10822-010-9346-4

    Google Scholar 

  29. Anon (2007) Naming and indexing of chemical substances for Chemical Abstracts. Chemical Abstracts Service, Columbus

    Google Scholar 

  30. IUPAC Compendium of Chemical Terminology—the Gold Book. http://goldbook.iupac.org/index.html. Accessed 28 Feb 2010

  31. Oellien F, Cramer J, Beyer C, Ihlenfeldt W-D, Selzer PM (2006) J Chem Inf Model 46(6):2342

    Article  CAS  Google Scholar 

  32. Indigo, an organic chemistry tool kit from SciTouch. http://opensource.scitouch.net/indigo/bingo, http://opensource.scitouch.net/indigo/bingo/user_manual#tautomer_search, http://opensource.scitouch.net/downloads/bingo_user_manual.pdf. Accessed 28 Feb 2010

  33. Epik. http://www.schrodinger.com/products/14/4/. Accessed 28 Feb 2010

  34. Greenwood JR, Calkins D, Sullivan AP, Shelley JC (2010) J Comput-Aided Mol Des. doi:10.1007/s10822-010-9349-1

    Google Scholar 

  35. ChemAxon Standardizer. http://www.chemaxon.com/products/standardizer/. Accessed 28 Feb 2010

  36. Trepalin SV, Skorenko AV, Balakin KV, Nasonov AF, Lang SA, Ivashchenko AA, Savchuk NP (2003) J Chem Inf Comput Sci 43(3):852

    CAS  Google Scholar 

  37. Sayle RA, Delany JJ (1999) Canonicalization and Enumeration of Tautomers. Paper presented at EuroMUG99, Cambridge, UK, 28–29 Oct 1999

  38. Mercury. http://www.ccdc.cam.ac.uk/free_services/mercury/. Accessed 28 Feb 2010

  39. Pluto. http://www.ccdc.cam.ac.uk/support/documentation/#rpluto. Accessed 28 Feb 2010

  40. Shelley JC, Cholleti A, Frye LL, Greenwood JR, Timlin MR, Uchimaya M (2007) J Comput-Aided Mol Des 21(12):681

    Article  CAS  Google Scholar 

  41. ChemAxon tautomerization plugin. http://www.chemaxon.com/jchem/marvin/help/calculations/isomers.html#tautomer. Accessed 28 Feb 2010

  42. ChemAxon tautomer duplicate filtering search option. http://www.chemaxon.com/jchem/doc/user/query_searchoptions.html#tautomer_duplicate. Accessed 28 Feb 2010

  43. Tautomer generation. pKa based dominance conditions for generating dominant tautomers. http://www.chemaxon.com/conf/Tautomer_generation_A4.pdf. Accessed 28 Feb 2010

  44. Clark AM, Labute P. SD File Processing with MOE Pipeline Tools. http://www.chemcomp.com/journal/sdtools.htm. Accessed 28 Feb 2010

  45. LigPrep. http://www.schrodinger.com/products/14/10/. Accessed 28 Feb 2010

  46. CCDC search example. http://www.ccdc.cam.ac.uk/products/csd_system/conquest/faqs/scientific_faq.php#tautomers. Accessed 28 Feb 2010

  47. Cruz-Cabeza AJ, Schreyer A, Pitt WR (2010) J Comput-Aided Mol Des. doi:10.1007/s10822-010-9345-5

    Google Scholar 

  48. InfoChem search tutorial. http://www.infochem.de/content/downloads/icfsetutorial.pdf. Accessed 28 Feb 2010

  49. Markush DARC. http://www.questel.com/customersupport/userdoc/docpdf/Thomson_Markush_Darc_User_Manual.pdf. Accessed 28 Feb 2010

  50. Town WG (1989) In: Warr WA (ed) Chemical structure information systems. ACS symposium series, vol 400. American Chemical Society, Washington, p 68

    Chapter  Google Scholar 

Download references

Acknowledgments

I am indebted to the many people who supplied data for this article, and in particular I would like to thank Jonathan Brecher of CambridgeSoft and Geoff Skillman of OpenEye for helpful discussions, Russ Hillard and Keith Taylor of Symyx for drafting two figures, and Thomson Reuters for some careful proof reading.

Author information

Authors and Affiliations

  1. Wendy Warr & Associates, Cheshire, England, UK

    Wendy A. Warr

Authors
  1. Wendy A. Warr
    View author publications

    You can also search for this author inPubMed Google Scholar

Corresponding author

Correspondence to Wendy A. Warr.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Warr, W.A. Tautomerism in chemical information management systems. J Comput Aided Mol Des 24, 497–520 (2010). https://doi.org/10.1007/s10822-010-9338-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10822-010-9338-4

Keywords