UPDATE (3/21) – I was contacted by the author of the paper who pointed out that my analysis was based on a misunderstanding of the paper. Specifically The primary goal of WES is to identify actives – and according to the authors definition, the most interesting actives (that should be ranked highly) are those that […]
Accessing Chemistry on the Web Using Firefox
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 […]
Which Datasets Lead to Predictive Models?
I came across a recent paper from the Tropsha group that discusses the issue of modelability – that is, can a dataset (represented as a set of computed descriptors and an experimental endpoint) be reliably modeled. Obviously the definition of reliable is key here and the authors focus on a cross-validated classification accuracy as the […]
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 […]