This is a follow on to my previous post that described a recent paper where we explored a few ways to characterize the differential activity of small molecules in dose response screens. In this post I wanted to highlight some aspects of this type of analysis that didn’t make it into the final paper. TL;DR […]
Analysing Differential Activity in Dose Response Screens
My colleagues and I recently published a paper where we explored a few methods to identify differential behavior in dose response screens. While there is an extensive literature about analyzing differential effects in genomic data (e.g. mciroarrays, RNAseq), these methods are based on distributional assumptions that holds for genomic data. This is not necessarily the […]
Call For Papers: Shedding Light on the Dark Genome – Methods, Tools & Case Studies
252nd ACS National Meeting Philadelphia, Aug 21-25, 2016 CINF Division Dear Colleagues, we are organizing a symposium at the Fall ACS meeting in Philadelphia focusing on computational, experimental and hybrid approaches to characterizing the unstudied and understudied druggable genome. In 2014 the NIH initiated a program titled, “Illuminating the Druggable Genome” (IDG) with the goal of improving our understanding […]
vSDC, Rank Products and DUD-E
This post is a follow-up to my previous discussion on a paper by Chaput et al. The gist of that paper was that in a virtual screening scenario where a small number of hits are to be selected for followup, one could use an ensemble of docking methods, identify compounds whose scores were beyond 2SD […]
Hit Selection When You’re Strapped for Cash
I came across a paper from Chaput et al that describes an approach to hit selection from a virtual screen (using docking), when follow-up resources are limited (a common scenario in many academic labs). Their approach is based on using multiple docking programs. As they (and others) have pointed out, there is a wide divergence […]