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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