An InChI (or see the FAQ) is a line notation for a molecular structure that was recently developed by the NIST and the IUPAC. Principally they can be applied to protein too (see below), but because proteins would give lenghty InChI’s and are quite well defined in terms of connectivity anyway, those can better be described by their amino acid sequence.
As of April 3, I will be working as postdoc in the group of Christoph Steinbeck at the Cologne University BioInformatics Center, or simply CUBIC, for a year. Though no exact plans have been decided upon, the work will include CDK, CML, ontologies, Bioclipse, semantic web technologies, Jmol, and other interesting things. Research areas will at least include QSAR, but I hope to touch bits of bioinformatics too.
Dan (the original Jmol author) has an interesting blog series: How to make money from Open Source scientific software I, II and III. Three more blog items are in the planning. The deal with how to make money from open source scientific software. He wants to be able to skeptically review the software in his field, hence open source.
The beta has been using Jmol as one of the viewers for ages already, but this beta is no longer: it’s the new interface for the PDB database.
Geldenhuys et al. published an article in Drug Discovery Today titled Optimizing the use of open-source software applications in drug discovery (DOI:10.1016/S1359-6446(05)03692-5), and approached the review from a bench chemist point of view. Unfortunately, he discusses free, but closed source, program in one go.
After Kalzium and kfile_chemical , KDE has now be extended with kparts for 3D structure and spectrum display: Kryomol . It is written in C++ and licensed GPL. It supports several chemistry formats, among which quantum chemical formats like Gaussian03, NwChem and ACES, and 3D structures as MDL molefile and XYZ.
A few days back, Classpath 0.90 was released, the first release after the 0.20 release. Earlier Classpath releases could run the rendering engine , but running the application failed so far .
With quite some help from Ola (thanx!), I made good progress with the CMLRSS plugin . The current result looks like:
Earlier I reported about postgenomic.com , and needed some diversion from my manuscript work (could no longer think straight about the article I’m working on). So time for some reading up on new technologies. Timing was perfect, because the source code of postgenomic.com got just uploaded to SourceForge SVN.
Earlier I already reported that student text books were picking up Jmol as 3D viewer. Now, Nature Structural & Molecular Biology reports (DOI:10.1038/nsmb0206-93) that they picked it up too, using FirstGlance in Jmol (thanx Peter, for reporting this on the Blue Obelisk mailing list!). And, thanx Eric, for acknowledging the hard work of the Jmol developers.
For the past few weeks I have been working on a review article, which will contain a section with new QSAR/QSPR descriptors published in the period 2000-now.