ChEMBL in RDF and Other Musings

Earlier today, Egon announced the release of an RDF version of ChEMBL, hosted at Uppsala. A nice feature of this setup is that one can play around with the data via SPARQL queries as well as explore the classes and properties that the Uppsala folks have implemented. Having fiddled with SPARQL on and off, it […]

A GPL3 Oracle Cheminformatics Cartridge

Sometime back I had mentioned a new cheminformatics toolkit, Indigo. Recently, Dmitry from SciTouch let me know that they had also developed Bingo, an Oracle cartridge based on Indigo, to perform cheminformatics operations in the database. This expands the current ecosystem of Open Source database cartridges (PGChem, MyChem, OrChem) which pretty much covers all the […]

Chemistry in Google Docs

I met with Jean-Claude Bradley yesterday and we had a pretty useful hack session, allowing him to easily incorporate chemical and cheminformatics functionality into a GoogleDocs spreadsheet. A common task that Jean-Claude wanted to automate was the calculation of milligrams (or milliliters) of a chemical required for a certain molarity.  So what we need for […]

AJAX’ified Pub3D

Pub3D is a 3D version of PubChem, in which we have generated a single conformer for 99% of PubChem using the smi23d suite of programs. The structures are then stored in a PostgreSQL database along with their distance moment shape descriptors described by Ballester and Graham-Richards. This allows us to perform shape similarity queries against […]