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 […]
Life and death in a screening campaign
So, how do I enjoy my first day of furlough? Go out for a nice ride. And then read up on some statistics. More specifically, I was browsing the The R Book and came across survival models. Such models are used to characterize time to events, where an event could be death of a patient […]
PAINS Substructure Filters as SMARTS
Sometime back Baell et al published an interesting paper describing a set of substructure filters to identify compounds that are promiscuous in high throughput biochemical screens. They termed these compounds Pan Assay Interference Compounds or PAINS. There are a variety of functional groups that are known to be problematic in HTS assays. The reasons for […]
Automating the Screening Pipeline
A key feature of high throughput screening (HTS) efforts is automation. The NCGC is no stranger to automation, with two Kalypsys robots and a variety of automated components such as liquid handlers and so on. But while the screen itself is automated, the transitions between subsequent steps are not. Thus, after a screen is complete, […]
Some More Comparisons with the GSK Dataset
My previous post did a quick comparison of the GSK anti-malarial screening dataset with a virtual library of Ugi products. That comparison was based on the PubChem fingerprints and indicated a broad degree of overlap. I was also interested in looking at the overlap in other feature spaces. The simplest way to do this is […]