Egon Willighagen

[Bernard
Munos](http://www.nature.com/nrd/journal/vaop/ncurrent/authors/nrd2131.html)
at [Eli Lilly & Co.](http://www.lilly.com/) wrote up a lengthy analysis
on open source in drug discovery in [Nature Reviews Drug
Discovery](http://www.nature.com/nrd/index.html): Can open-source R&D
reinvigorate drug research?
(DOI:[10.1038/nrd2131](https://doi.org/10.1038/nrd2131)). When scanning
the article I saw this quote:

*Other tools such as eMolecules, Jmol or the Chemistry Development Kit
are adding powerful chemical search and visualization capabilities to
the open-source scientist's toolbox.*

Unfortunately, the paper does not point to the correct [CDK
website](http://cdk.sf.net/), but to the CUBIC backend at
<http://almost.cubic.uni-koeln.de/cdk>. Moreover, I don't think the
quote does full justice to what the CDK has achieved in the past six
years; I'm sure we have achieved more than a fingerprinter and some 2D
and 3D rendering!

#### References

- [10.1038/nrd2131](https://doi.org/10.1038/nrd2131)


Bernard Munos at Eli Lilly &amp; Co. wrote up a lengthy analysis on open source in drug discovery in Nature Reviews Drug Discovery: Can open-source R&amp;D reinvigorate drug research?

"Jmol and the CDK add powerful chemical capabilities", says Munos in Nature Reviews Drug Discovery

Geldenhuys et al. published an article in [Drug Discovery
Today](http://www.sciencedirect.com/science/journal/13596446) titled
*Optimizing the use of open-source software applications in drug
discovery*
(DOI:[10.1016/S1359-6446(05)03692-5](https://doi.org/10.1016/S1359-6446(05)03692-5)),
and approached the review from a bench chemist point of view.
Unfortunately, he discusses free, but closed source, program in one go.

He discusses the advantages and problems with opensource, and mentions
the often lacking user-friendly GUI (true), and the the lack of
literature to validate the program. It was unclear to me wether the last
argument applied to the free tools, or to the open source programs; I
thought the open-source projects like the [CDK](http://cdk.sf.net/),
[JOELib](http://joelib.sf.net/), [Jmol](http://www.jmol.org/) and
[PyMol](http://pymol.sf.net/) were quite strong in this area, at least
compared to the commercial software I have seen.

#### References

- [10.1016/S1359-6446(05)03692-5](https://doi.org/10.1016/S1359-6446(05)03692-5)


Geldenhuys et al. published an article in Drug Discovery Today titled
<em>
 Optimizing the use of open-source software applications in drug discovery
</em>
(DOI:10.1016/S1359-6446(05)03692-5), and approached the review from a bench chemist point of view.

Messaggi di Rogue Scholar

"Jmol and the CDK add powerful chemical capabilities", says Munos in Nature Reviews Drug Discovery

Open source in drug discovery