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  • Willighagen, Egon L.Maastricht Univ, Dept Bioinformat, NUTRIM, BiGCaT, NL-6200 MD Maastricht, Netherlands. (author)

The Chemistry Development Kit (CDK) v2.0 : atom typing, depiction, molecular formulas, and substructure searching

  • Article/chapterEnglish2017

Publisher, publication year, extent ...

  • 2017-06-06
  • Springer Science and Business Media LLC,2017
  • electronicrdacarrier

Numbers

  • LIBRIS-ID:oai:DiVA.org:uu-330735
  • https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-330735URI
  • https://doi.org/10.1186/s13321-017-0220-4DOI

Supplementary language notes

  • Language:English
  • Summary in:English

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Classification

  • Subject category:ref swepub-contenttype
  • Subject category:art swepub-publicationtype

Notes

  • Correction in: Journal of Cheminformatics 2017 9:53https://doi.org/10.1186/s13321-017-0231-1
  • Background: The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform computations on them. The library implements a wide variety of cheminformatics algorithms ranging from chemical structure canonicalization to molecular descriptor calculations and pharmacophore perception. It is used in drug discovery, metabolomics, and toxicology. Over the last 10 years, the code base has grown significantly, however, resulting in many complex interdependencies among components and poor performance of many algorithms.Results: We report improvements to the CDK v2.0 since the v1.2 release series, specifically addressing the increased functional complexity and poor performance. We first summarize the addition of new functionality, such atom typing and molecular formula handling, and improvement to existing functionality that has led to significantly better performance for substructure searching, molecular fingerprints, and rendering of molecules. Second, we outline how the CDK has evolved with respect to quality control and the approaches we have adopted to ensure stability, including a code review mechanism.Conclusions: This paper highlights our continued efforts to provide a community driven, open source cheminformatics library, and shows that such collaborative projects can thrive over extended periods of time, resulting in a high-quality and performant library. By taking advantage of community support and contributions, we show that an open source cheminformatics project can act as a peer reviewed publishing platform for scientific computing software.

Subject headings and genre

Added entries (persons, corporate bodies, meetings, titles ...)

  • Mayfield, John W.NextMove Software Ltd, Cambridge CB4 0EY, England. (author)
  • Alvarsson, Jonathan,1981-Uppsala universitet,Institutionen för farmaceutisk biovetenskap(Swepub:uu)jonal195 (author)
  • Berg, ArvidUppsala universitet,Institutionen för farmaceutisk biovetenskap(Swepub:uu)arvbe873 (author)
  • Carlsson, LarsAstraZeneca, Innovat Med & Early Dev, Quantitat Biol, Molndal, Sweden. (author)
  • Jeliazkova, NinaIdeaconsult Ltd, A Kanchev 4, Sofia 1000, Bulgaria. (author)
  • Kuhn, StefanUniv Leicester, Dept Informat, Leicester, Leics, England. (author)
  • Pluskal, TomasWhitehead Inst Biomed Res, 455 Main St, Cambridge, MA 02142 USA. (author)
  • Rojas-Cherto, MiquelQuim Clin Aplicada, Amposta 43870, Spain. (author)
  • Spjuth, Ola,1977-Uppsala universitet,Institutionen för farmaceutisk biovetenskap,4 Hanway Pl, London W1T 1HD, England.(Swepub:uu)olspj499 (author)
  • Torrance, Gilleain4 Hanway Pl, London W1T 1HD, England. (author)
  • Evelo, Chris T.Maastricht Univ, Dept Bioinformat, NUTRIM, BiGCaT, NL-6200 MD Maastricht, Netherlands. (author)
  • Guha, RajarshiNatl Ctr Adv Translat Sci, 9800 Med Ctr Dr, Rockville, MD 20850 USA. (author)
  • Steinbeck, ChristophFriedrich Schiller Univ, Inst Inorgan & Analyt Chem, Lessingstr 8, D-07743 Jena, Germany. (author)
  • Maastricht Univ, Dept Bioinformat, NUTRIM, BiGCaT, NL-6200 MD Maastricht, Netherlands.NextMove Software Ltd, Cambridge CB4 0EY, England. (creator_code:org_t)

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  • In:Journal of Cheminformatics: Springer Science and Business Media LLC91758-2946

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