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Saturday, August 27, 2016

cAMP as a signalling compound?

cAMP. Picture from Wikipedia.
Maastricht University gives me the opportunity to study how chemical differences between individuals affect the metabolism, particularly for humans (I'm a chemist working in biology). Reading biological literature and text books sometimes makes my jaw drop. Biology is beautifully complex and sometimes just doesn't make sense at all.

So, in my WTF-moment of the day, I was reading about various RNA, then nucleotides, etc, and got to cAMP. This, and I know that from WikiPathways too, can act as a secondary signalling compound: membrane receptor passes the signal on to cAMP. But then? I mean, one single molecule. Supposed to give a variety of signals. How?? How can it be selective? How is the hormone-specific signal not lost when passing the cytoplasma?? Or is it just a general "ALERT ALERT, SOMETHING OUTSIDE HAPPENED"?

Back to the book.

Monday, August 15, 2016

Alzheimer’s disease, PaDEL-Descriptor, CDK versions, and QSAR models

A new paper in PeerJ (doi:10.7717/peerj.2322) caught my eye for two reasons. First, it's nice to see a paper using the CDK in PeerJ, one of the journals of an innovative, gold Open Access publishing group. Second, that's what I call a graphical abstract (shown on the right)!

The paper describes a collection of Alzheimer-related QSAR models. It primarily uses fingerprints and the PaDeL-Descriptor software (doi:10.1002/jcc.21707) for it particularly. I just checked the (new) PaDeL-Descriptor website and it still seems to use CDK 1.4. The page has the note "Hence, there are some compatibility issues which will only be resolved when PaDEL-Descriptor updates to CDK 1.5.x, which will only happen when CDK 1.5.x becomes the new stable release." and I hope Yap Chun Wei will soon find time to make this update. I had a look at the source code, but with no NetBeans experience and no install instructions, I was unable to compile the source code. AMBIT is now up to speed with CDK 1.5, so the migration should not be too difficult.

Mind you, PaDEL is used quite a bit, so the impact of such an upgrade would be substantial. The Wiley webpage for the article mentions 184 citations, Google Scholar counts 369.

But there is another thing. The authors of the Alzheimer paper compare various fingerprints and the predictive powers of models based on them. I am really looking forward to a paper where the authors compare the same fingerprint (or set of descriptors) but with different CDK versions, particularly CDK 1.4 against 1.5. My guess is that the models based on 1.5 will be better, but I am not entirely convinced yet that the increased stability of 1.5 is actually going to make a significant impact on the QSAR performance... what do you think?


Simeon, S., Anuwongcharoen, N., Shoombuatong, W., Malik, A. A., Prachayasittikul, V., Wikberg, J. E. S., Nantasenamat, C., Aug. 2016. Probing the origins of human acetylcholinesterase inhibition via QSAR modeling and molecular docking. PeerJ 4, e2322+. 10.7717/peerj.2322

Yap, C. W., May 2011. PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints. Journal of Computational Chemistry 32 (7), 1466-1474. 10.1002/jcc.21707

Saturday, August 13, 2016

The Groovy Cheminformatics scripts are now online

My Groovy Cheminformatics with the Chemistry Development Kit book sold more than 100 times via Lulu.com now. An older release can be downloaded as CC-BY from Figshare and was "bought" 39 times. That does not really make a living, but does allow me to financially support CiteULike, for example, where you can find all the references I use in the book.

The content of the book is not unique. The book exists for convenience, it explains things around the APIs, gives tips and tricks. In the first place for myself, to help me quickly answer questions on the cdk-user mailing list. This list is a powerful source of answers, and the archive covers 14 years of user support:


One of the design goals of the book was to have many editions allowing me to keep all scripts updated. In fact, all scripts in the book are run each time I make a new release of the book, and, therefore, which each release of the CDK that I make a book release for. That also explains why a new release of the book currently takes quite a bit of time, because there are so many API updates at the moment, as you can read about in the draft CDK 3 paper.

Now, I had for a long time also the plan to make the scripts freely available. However, I never got around to making the website to go with that. I have given up on the idea of a website and now use GitHub. So, you can now, finally, find the scripts for the two active book releases on GitHub. Of course, without the explanations and context. For that you need the book.

Happy CDK hacking!