Copyright©2008 Antony Williams
ChemSpider has been helped by a number of organizations either with their guidance, their sponsorship support or, in the case of commercial software vendors, by the contribution of software “to the cause”. I have watched ChemAxon for a number of years. When I first saw them at an ACS meeting I was impressed with not only their relationship building, their growing following but also with their deep understanding of many of the challenges in delivering a cheminformatics toolkit. I commented then to “Watch these guys”. And I DID mean it as a “look over your shoulder” type of way. Over the years I have only been more impressed with their ability to deliver and especially with their contributions to academia with their Application Package software. Most people know them for their Marvin structure drawing package, now in its latest form. There are many websites where you will happen across their branding. I sat in recently on a presentation regarding their JChemBase platform and was very impressed with the flexibility, speed and interface.
We have now been given access to a number of their software components and, with time, you will see us use more of their software. We have to figure out integration etc and balance it with all of the other tasks waiting on us. For now I wanted to comment that we recently used ChemAxon’s 3D structure optimizer to produce 3D structures for two purposes…to put onto the database to pass to JMol for visualization purposes and to provide a feed to the LASSO algorithms. The algorithms were fast enough for us to pass through almost 20 million molecules. We were provided access to a computer cluster to do these calculations thankfully. We did set rather stringent criteria in terms of time so not every structure on the database is optimized – if they weren’t done in a certain period we would abort and move to the next. When there are resources available we will pass the incomplete set through again.
My personal thanks to ChemAxon for their support. It’s greatly appreciated by us and, I am sure, our users too.Stumble it!