ChemSpider Blog

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.

I’ve commented previously about the fact that Microsoft had used our web services to connect to Infomesa (1,2). Last week I had a chance to meet with Sam Batterman face-to-face for an overview of Infomesa and to see the services in action. Sam and I chatted for a couple of hours about his platform, the challenges of managing quality in publicly accessible data (and not proliferating errors) and the directions for ChemSpider in general and whether we could extend the services to support his needs.

Infomesa is a BIG whiteboard. And I mean BIG! During our discussions Sam threw up photos, charts, spreadsheets and videos onto the board and formed relationships between them. He demonstrated using our services to pull back/generate SMILES strings,  structure images and InChIKeys. He demonstrated mapping relationships as I would do today in MindManager. I could see immediate utility to the approach of the giant whiteboard. I am tired of arranging relationships over multiple documents and while I like MindManager a lot (!) the utility of the enormous whiteboard approach (I think Sam mentioned “equivalent to 50,000 pixels”) became clear in a couple of minutes.

I look forward to playing with Infomesa myself when it’s available and doing what we can through our web services to help offer additional utility to chemists.

On a very regular basis I receive requests now from ChemSpider users for what I would call “General Help”. Here’s a request from a user to answer a Chemistry Question. Can the community help?

“We have detected 2,2 Dichloropropionic Acid  in several of our drinking water systems at levels of about 0.1 to 0.2 ug/L (above the EU MCL), but none in the source water (in some cases surface water, in others, groundwater under the direct influence of surface water).  The levels in the pipe rise after the addition of free chlorine.  This leads me to believe that either some sort of lab interference or some other compound is actually being detected.  We have sent samples to two separate labs using two different methods (blanks were not sent) and the results were confirmed.

Any thoughts on how 2,2 Dichloropropionic Acid might be naturally formed in the presence of chlorine in drinking water? Is it possible that other organics either degrade down to 2,2 Dichloropropionic Acid or are precursors for 2,2 Dichloropropionic Acid, in the presence of chlorine?”

Please post your comments on this blog and I will ask the user to watch this page.

This is part of our future endeavors. Shortly we will establish a discussion forum for ChemSpider users so that when a user has scientific problems you can post here and discuss. Should the outcome from the discussion be science associated with a particular chemical we will add it to a record n the database for further reference.