"Jmol and the CDK add powerful chemical capabilities", says Munos in Nature Reviews Drug Discovery

Bernard Munos at Eli Lilly & Co. wrote up a lengthy analysis on open source in drug discovery in Nature Reviews Drug Discovery: Can open-source R&D reinvigorate drug research? (DOI:10.1038/nrd2131). When scanning the article I saw this quote: less than 1 minute read

Chemical Archeology: OSCAR3 to NMRShiftDB.org

Chemical Archeology (see Christoph’s comment) is the process of extracting chemical information from old journal articles. Some time ago, Peter Corbett from the group of Peter Murray-Rust visited the CUBIC to talk to us about Oscar3 which can do just that. That day, we already hooked OPSIN into Bioclipse . 2 minute read

BioJava 1.5 beta released

Martin Szugat reported that a beta for BioJava 1.5 has been released. New features include: a new biojavax package with extension on the basic functionlity, such as the RichSequence.IOTools and the RichSequence object; a genetic algorithm library; features that allow manipulation of 3D structure files and objects; and non-HMM implementations of the NW and SW alignment algorithms. The announcement also mentions a new package for handling external processes (org.biojava.utils.process); I am wondering what that is about. I will upload this beta to Bioclipse trunk/bc_biojava/ shortly, so that we can play with it. less than 1 minute read

Calculating geometrical properties with the CDK

ケムインフォマティクスに虚空投げ runs a story on how to calculate geometrical properties of a 3D structure using CDK’s ForceFieldTools. This class contains a few methods to calculate distances between atoms and angles between bonds. less than 1 minute read

R News special issue on chemistry

R News just released a special issue on the use of the versatile statistics program R in chemistry. It features six articles amongst which one by Rajarshi Guha on the CDK-R bridge, and one by my supervisor and me on the use of self-organizing maps to cluster crystal structures. less than 1 minute read

Chemical blogspace

We all know chemical space; Chemical blogspace (Cb) is different: it is the chemistry discussed in blogspace. Cb is build on the opensource software of Postgenomic.com which I bloged on before. The now running Cb aggregates 19 blogs and, like the original, extracts linked (cited or reviewed) articles from literature. less than 1 minute read

Bioclipse gets a new extension point

I hacked in a new extension point for Bioclipse yesterday, based on a proposal I made earlier. The new extension point (EP) is called ChildResourceCreator and allows creating child resources for a given IBioResource. One application where this is very useful is the CMLRSS application (earlier blog), or any RSS or Atom enriched with any other XML language. Here, child resources are created for each feed entry resource with as content the foreign XML, e.g. the CML bits in the blog. 1 minute read