Skip to content


  • Oral presentation
  • Open Access

Making sure there's a "give" associated with the "take": producing and using open-source software in big pharma

  • 1Email author,
  • 1,
  • 2,
  • 1 and
  • 1
Journal of Cheminformatics20113 (Suppl 1) :O3

  • Published:


  • Molecular Modeling
  • Research Organization
  • Practical Aspect
  • Production Environment
  • Large Research

In contrast to bioinformatics, open-source software is not as widely used in the pharmaceutical industry for molecular modeling and cheminformatics. Typical reasons given for this include problems with code quality, stability, and long-term support for the software (somehow this is less of a concern with bioinformatics software... kind of makes one think). Recently, our group has started making heavy use of an open-source cheminformatics toolkit RDKit [1] in our production environment. Importantly, we are not just acting as consumers of open-source software -- we are active members of the open-source community and have support from management to contribute code back to the project.

In this presentation we will provide a brief overview of the RDKit itself and then present a number of case studies of how we have made use of this open-source platform. Examples will include using the toolkit for method development [2, 3], integration with proprietary tools, and some recent (and upcoming) contributions to the open-souce community, including a database cartridge for fast and flexible similarity searching in the open-source PostgreSQL database [4], and adding support for the RDKit within the open-source pipelining platform Knime [5]. We will finish with a discussion of some practical aspects of working on and with open-source tools in a large research organization.

Authors’ Affiliations

Novartis Institutes for BioMedical Research, Basel, CH-4002, Switzerland
Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA


  1. RDKit: open-source cheminformatics.,
  2. Vulpetti A, Hommel U, Landrum G, Lewis R, Dalvit C: Design and NMR-Based Screening of LEF, a Library of Chemical Fragments with Different Local Environment of Fluorine. J. Am Chem. Soc. 2009, 131: 12949-12959. 10.1021/ja905207t.View ArticleGoogle Scholar
  3. Vulpetti A, Landrum G, Ruedisser S, Erbel P, Dalvit C: 19F NMR Chemical Shift Prediction with Fluorine Fingerprint Descriptor. J. of Fluorine Chem. 2010, 131: 570-577. 10.1016/j.jfluchem.2009.12.024.View ArticleGoogle Scholar
  4. PostgreSQL :,
  5. KNIME :,