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. […]

Drug-Target Networks & Polypharmacology

I came across Takigawa et al where they address polypharmacology by investigating drug-target pairs. ┬áTheir approach is to simultaneously identify substructures from the ligand and subsequences from the target and combine this information to suggest drug-target pairs that represent some form of polypharmacology. ┬áMore specifically their hypothesis is that “polypharmacological principles” are embedded in a […]

Annotating Bioassays

I’ve been working for some time with the PubChem Bioassay collection – a set of 1293 assays that cover a range of techniques (enzymatic, phenotypic etc.), targets and sizes (from 20 molecules to 200,000 molecules). In addition, some assays are primary, high-throughput assays whereas a number of them are smaller, confirmatory assays. While an extremely […]