The topic of algorithmic fairness has started recieving a lot of attention due to the ability of predictive models to make decisions that might discriminate against certain classes of people. The reasons for this include biased training data, correlated descriptors, black box modeling methods or a combination of all three. Research into algorithmic fairness attempts […]
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 […]
Cryptography & Chemical Structure Search
Encryption of chemical information has not been a very common topic in cheminformatics. There was an ACS symposium in 2005 (summary) that had a number of presentations on the topic of “safe exchange” of chemical information – i.e., exchanging information on chemical structures without sharing the structures themselves. The common thread running through many presentations was to […]
Maximally Bridging Rings (or, Doing What the Authors Should’ve Done)
Recently I came across a paper from Marth et al that described a method based on network analysis to support retrosynthetic planning, particularly for complex natural products. I’m no synthetic chemist so I can’t comment on the relevance or importance of the targets or the significance of the proposed approach to planning a synthetic route. […]