Joe Leonard posted a question on the CCL mailing list today regarding “conformation envelopes”. More specifically, he asked Has there been work on creating visualizations of “conformer envelopes”, graphical representations of the conformational space occupied (or available) to molecules. Particularly when such visualizations are used to (quickly/visually) compare whether 2 molecules can adopt the same […]
Live ONS Solubility Queries
In a previous post, I described a simple web form to query and visualize the solubility data being generated as part of the ONS Challenge. The previous approach required me to manually download the data and load it into a Postgres database. While trivial from a coding point of view, it’s a pain since I […]
Kinase Inhibitors and Polypharmacology
The Curious Wavefunction has a nice post on the issue of selective and non-selective kinase inhibitors. An interesting commentary, especially in the light of the recent paper on network polypharmcology. While there have been a number of papers on polypharmcology and the idea itself is very attractive, it has seemed to me that for this […]
Depicting SMILES Dynamically
Sometime back I was playing around with dynamic HTML and cam across a tutorial that described how to implement the dynamic suggestion feature that is commonly found on many websites (such as Google and Amazon). This set me wondering how I could use this mechanism to dynamically depict a SMILES string as I type it.
Do the CDK Fingerprints Work?
In a previous post, I dicussed virtual screening benchmarks and some new public datasets for this purpose. I recently improved the performance of the CDK hashed fingerprints and the next question that arose is whether the CDK fingerprints are any good. With these new datasets, I decided to quantitatively measure how the CDK fingerprints compare […]