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. Their 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. More specifically their hypothesis is that “polypharmacological principles” are embedded in a […]
Getting the GO into a Graph Data Structure
Today while working on a project I needed to get access to the Gene Ontology hierarchy. While there a number of GO browsers such as Amigo, I needed access to the raw data to generate a graph that I could then slice and dice. A few minutes with Python led to a simple solution. The […]
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 […]
SALI Viewer Now on GitHub
Last year, John Van Drie and I published two papers (here and here) on the Structure Activity Landscape Index, (SALI) which is a way to view SAR data as a network of compounds. Along with the paper ,I put up a simple Java application (licensed under the LGPL) to generate and explore these networks. – […]