Two weeks ago the write up of a week-long scientific discussions around artificial intelligence for natural product drug discovery in Leiden at the Lorentz Center got published (doi:10.1038/s41573-023-00774-7, free PDF). Sadly, the meetings was still during the (partial) lockdown, and I think my contribution could have been more extensive.

For the past few weeks I have been working on a review article, which will contain a section with new QSAR/QSPR descriptors published in the period 2000-now.

If you have read my previous post and visited that other blog, you might have noted the Technorati keywords . Or tags, really, as explained in this rel=“tag” microformat. Adding them to blog items, will enable indexing by Technorati, one of the bigger blog search engines. So, from now on, you’ll see these tags in my items too, hoping they don’t get annoying.

About two years ago a student started with me to work on the use of 1D NMR and IR spectra in quantitative structure-activity relationship (QSAR) work, with the goal to show that these spectra contain 3D information relevent to QSAR models. It is known that these spectra depend on the 3D conformation of the molecule.

Derek Lowe is the author of the blog In the Pipeline which is really fun to read. Derek works in pharmaceutical industry and gives a great insight in how things work in that field of molecular sciences. Yesterday he blogged about What Makes an Ugly Molecule? , and touches the Rule-of-Five, the hydrochloric acid bath (aka stomach), and other reasons that make molecules ugly.

In a recent JCIM article, Schuffenhauer compares a few subset selection methods, and notes that some of them reduce the average complexity of the molecules. They put this in relation to other research that states that lead compounds with high complexity have higher activities. Recommended reading material for the holidays.

For some weeks now I have been thinking about bug 1309731: “ModelBuilder3D overwrites Atom IDs”. The ModelBuilder3D is a complex piece of source code, reusing many other parts of the CDK, including atom type perception. Somewhere in October, however, I found that Taverna could not create 3D models and convert these into reasonable CML because the Atom ID’s were messed up. So the question is, where did the ModelBuilder3D do this?

This evening I have been looking at with the KNOPPIX customization howto, and ran many of the interesting commands. I’ve setup a environment with Kalzium, OpenBabel, CDK, jython, PyMOL, and for development I included gcj and Eclipse. At some later point I will include kfile_chemical too, but I want to make a deb package first.

OK, just back from the first German Chemoinformatics Conference, which I enjoyed very much. A rather interesting program, and lots of interesting posters too. You can read the programme online, and will not spend too many words on that (at least not now). But what I will do is point out some interesting posters here. One poster was on the Molecular Query Language (MQL) by Ewgenij Proschak from Frankfurt.

This sunday starts the first German Chemoinformatics Conference in Goslar. It’s an interesting programme , with presentations on the InChI, PubChem, 25 years of chemoinformatics, the chemical semantic web, and much more. Among these presentations is mine, on comparing crystal structures (PDF ) and deducing cell parameters. But I’m having a poster on QSAR too.