Inter- and Extrapolation: the NMR shift prediction debate

Chemical blogspace has seen a lengthy discussion on the quality of a few NMR shift prediction programs, and Ryan wanted to make a final statement. Down his blog item he had this quote from Jeff, discussing the use of the NMRShiftDB as external test set:

4 minute read

That big pile of paper...

Everyone of use knows that big pile of paper on your desk that contains the things we want to read, scan or just browse. I even have an electronic equivalent. Another pile contains leaflets and glossy folders from conferences, like the ACS meeting in Chicago. OK, going to get rid of those last ones, and will shortly put the links here.

1 minute read

Standing on the shoulders of ... the Blue Obelisk

The Seven stones wondered what to do with a petaflop in science, in response to Declan’s The petaflop challenge in Nature. Declan discusses in this commentary the increase in computing power and the necessity of parallel programming to make use of it. Now, I do have some ideas (e.g. enumerating metabolomic space, mining the RDF graph of our collective biological and chemical knowledge base for the one hundred most supported contradictions), but that is not what I want to talk about. It is this fragment from Declan’s piece:

2 minute read

Atom typing in the CDK

Atom typing is one of principal activities in chemoinformatics. Atom types provide additional information that cannot be derived from the connection table that is being used, or may define what force fields terms should be used. This makes perception of atom types very important.

2 minute read

Chemical RDFa with Operator in the Firefox toolbar

December last year I proposed the use of microformats and RDFa for simple semantic markup of molecular information. I linked that with the InChI extension for the Postgenomic.com software for Chemical blogspace and wrote these tools to work with the markup:

2 minute read

QSAR plugin for Bioclipse getting in shape

Over the last few weeks I continued the work on getting (descriptor-based) QSAR/QSPR implemented in Bioclipse. JOELib (GPL) and the CDK (LGPL) being two prominent opensource engines that can calculate molecular descriptors, and AMBIT a front-end.

1 minute read

Test File Repository and RelaxNG

Last week I started the Blue Obelisk Chemical Test File Repository, a repository of OSI-approved-licenced test files (from various sources) to improve interoperability between chemoinformatics software.

1 minute read