Friday, January 26, 2007

Cb gets a CMLRSS feed

My Chem-bla-ics blog contains a couple of blog items about CMLRSS, that is RSS feeds enriched with Chemical Markup Language. Some time ago, I wrote a plugin for CMLRSS for Bioclipse, as replacement for the Jmol and JChemPaint plugins shown in the CMLRSS article (DOI:10.1021/ci034244p).

Now, since I was looking at some bug reports to fix for the upcoming Bioclipse 1.0.1 release, I discovered that the plugin did not work well with Atom 1.0 feeds from Because Chemical blogspace uses Atom 1.0 too, I wanted to extend the feed with latest molecules with CML content; that is, to make it a nice CMLRSS feed.

Molecules in Chemical blogspace

I mentioned the InChI extension of Chemical blogspace before, and worked a bit more on it today. For example, I only today discovered that the 'pagination' was not working. And, for some days, I wanted the Molecules page to show all molecules being discussed, not only those that are known in PubChem.
Finally, I fixed the sorting, so that the molecules are now sorted based on the post date of the blog item that cites the molecule. It now looks like this (note the molecule count, and that the second InChI does not have an image):

The CMLRSS feed of Chemical blogspace

The next step was to actually include CML in this feed. The CML is created with OpenBabel from a MDL molfile downloaded from PubChem. BTW, this CML can be accessed from the Molecules page too, as can be seen in the above screenshot.

After some tweaking of the Atom feed of Chemical blogspace, and having Bioclipse work with URLConnections for web servers that do not return a Content-Length: field, this was the result:

Tuesday, January 16, 2007

Red/Yellow, FDA alerts and other properties

Yvonne Martin recently wrote about, in her experience, what works and what does not work in chemoinformatics/computational chemistry (DOI:10.1002/qsar.200610102). She based her conclusions on the 17 month usage of services provided via webpages at Abbott. In that period, almost 3 million (unique?) molecules were processed, for which the following properties were requested most, among a few others:

  • red/yellow alerts
  • FDA mutagenicity alerts
  • logP
  • Rule-of-Five
  • pKa
  • total polar surface area
  • solubility
Some of these can be calculated easily, and I tend towards adding those to the Molecules section of Chemical blogspace. The red/yellow and FDA mutagenicity alerts require me to define a list of substructures, and suggestions are most welcome.

Martin discusses the limited accuracy of the computational calculation of LogP, pKa and other properties, but concludes that they are nevertheless used in deciding which compounds to synthesize.

Organic Chemists?

Now, these properties are mostly pharma oriented, and, therefore, I would like the organic chemists on our blogspace what properties you would like to see added.

Thursday, January 11, 2007

New Blogs #2

Since New Blogs #1, I have added these new blogs: