Sunday, 1 May 2011

Questions for On-line Cheminformatics Tutorial

Some time ago I set up an on-line cheminformatics tutorial based on the "Try Python" software of Michael Foord (see my blog post for details).

When a reader mentioned in passing that he found this tutorial useful for introducing people to cheminformatics concepts, it made me realise that it might actually be useful for something. And so, when I had to put together a practical on the subject of Cheminformatics a few weeks ago, I decided to use this tutorial as the basis. I had the students go through the tutorial and answer a series of questions based around each of the three main chapters (Introduction to Cinfony, Descriptors, and Fingerprints).

Does anyone have any suggestions for other cheminformatics practicals?

Notes: This is Windows and Mac only. "Try Python" should (but does not) run on Linux under Moonlight. The problem was reported to the Moonlight devs back in 2009.


Steve W said...

Great idea Noel.

This is kind of simple, but one thing you could add is to have them look at different file formats that might be used in a cheminformatics context like xyz, mol, sdf, cml or pdb. These files are similar to one another but slightly different, and include information not encoded in SMILES or InChI.

Or you could generate a molecule from a SMILES string, then look at the mol file before and after using the make3D method for instance.

Igor said...

This is exactly what I was looking for
to explain/showcase simple python scripting for chemistry!
I can also add that it works on a Mac 10.5
in Safari after Silverlight is installed.
No luck with Linux though.

Noel O'Boyle said...

Thanks for the suggestions and encouragement.

@Igor: I've updated the text to indicate Mac support.

Prashanth Athri said...

One idea maybe --
A QSAR/SAR type exercise, where you have them calculate properties using scripts and then correlate that with some independent variable in a known data set....
I have found that chemical propt calculations get students from a chem background excited.