I recently came across a paper by Yilancioglu et al that described a method to predict drug synergies using only lipophilicity. In effect, it claimed to predict synergy based purely on a physicochemical property and independent of target or pathway information. Their results suggest that combinations of two lipophilic drugs had a greater tendency to […]
Fingerprint Similarity Searches in MongoDB
A few of my recent projects have involved the use of MongoDB, primarily for the ease afforded by a schemaless environment. Sometime back I had investigated the use of MongoDB to store chemical structure data, though those efforts did not actually query structures per se; instead they queried for precomputed numeric or text properties. So […]
Ranking Dose Response Curves
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 […]