With the profusion of chemical information on the web – in the form of chemical names, images of structures, specific codes (InChI etc), it’s sometimes very useful to be able to seamlessly retrieve some extra information while browsing a page that contains such entities. The usual way is to copy the InChI/SMILES/CAS/name string and paste […]
Retrieving Target Classifications from ChEMBL
There are a number of scenarios when it’s useful to be able to classify protein targets – high level summaries, enrichment calculations and so on. There are a variety of protein classification schemes out there such as PANTHER, SCOP and InterPro. These schemes are based on domains and other structural features. ChEMBL provides it’s own […]
fingerprint 3.5.2 released
Version 3.5.2 of the fingerprint package has been pushed to CRAN. This update includes a contribution from Abhik Seal that significantly speeds up similarity matrix calculations using the Tanimoto metric. His patch led to a 10-fold improvement in running time. However his code involved the use of nested for loops in R. This is a well […]
Updated version of rcdk (3.2.3)
I’ve pushed updates to the rcdklibs and rcdk packages that support cheminformatics in R using the CDK. The new versions employ the latest CDK master, which as Egon pointed out has significantly fewer bugs, and thanks to Jon, improved performance. New additions to the package include support for the LINGO and Signature fingerprinters (you’ll need the […]
Support for feature,count fingerprints in fingerprint 3.5.0
I’ve just updated the fingerprint package to v3.5.0 (should show up on CRAN shortly, or else you can get it directly from my Github repository). The main update in this version is better support for feature,count type fingerprints. An example would be ECFP or signature fingerprints. In these types of fingerprints, the output is usually […]