Tuesday, September 12, 2006

Cheminformatics at ACS

Here is a little mid conference report from the American Chemical Society meeting (ACS fall 2006) in San Francisco. The Sunday CINF session on Cyberinfrastructure in Chemistry, Information and Education: New Emerging Technologies was the most interesting for me.

Evan Bolton gave a nice overview of PubChem. The slide that struck me the most was the graph showing the exponential rise of compounds and visitors during the past 12 months. There are now almost 13 million compounds in that database now. From an organic chemistry perspective PubChem has been of limited use to us because it does not generally have links to synthetic or spectral data for compounds, although the biological data is likely to become more useful as we move to the in vitro testing of our anti-malarial compounds. However, using the LinkOut feature in Entrez to annotate records may provide a mechanism to start doing that. PubChem is a very important project for chemical Open Source Science and its continued explosive growth is very encouraging.

Jeremy Frey talked about his CombeChem project, which involves learning about how chemists plan and execute experiments for the development of software and hardware to assist with that. I learned that Jeremy had published their experiments automatically to a blog but that their server is currently down. When he brings this back up I'll be sure to report on it in detail. We had the opportunity to discuss the possibility of collaborations over lunch. We both have an interest in developing anti-malarial agents and he has some docking software that may prove to be quite helpful to determine the affinity of some of our compounds for enoyl reductase. One of the problems is that the licensing terms of commercial software makes it difficult to share the results of the calculations openly. What we would like to do is run docking experiments as a web service at some point. That would be very useful for Open Source Science. Jeremy also gave a talk on Tuesday about his e-malaria project, where he has students try to design anti-malarial compounds.

Rene Deplanque alerted us to Chemgaroo and the Chemgapedia. Most of it is in German but they have translated the organic chemistry section to English and it is free for academic use. I've added it to the resources for my class this fall.
Christoph Steinbeck gave an interesting overview of the development of the NMRShiftDB to make NMR spectra openly available to everyone. It is very challenging to set up and run these volunteer based efforts.

Peter Murray-Rust talked about moving towards Open Data and Open Access. He described a system in place where X-ray Crystal structures are deposited and automatically become public after some time. That enables the researcher time to publish by traditional channels, while making it easy to obtain permission to make the data public by default. Peter wanted to give several demos, including the new version of Bioclipse. However, not having access to the internet made that difficult.

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