Joerg has made a nice blog post on the use of Open Source software and data to analyse the occurence of antithrombotics. More specifically he was trying to answer the question
Which XRay ligands are closest to the Fontaine et al. structure-activity relationship data for allowing structure-based drug design?
using Blue Obelisk tools and ChemSpider and where Fontaine et al. refers to the Fontaine Factor Xa dataset. You should read his post for a nice analysis of the problem. I just wanted to consider two points he had raised.