As part of my work at IU I have been implementing a number of cheminformatics web services. Initially these were SOAP, but I realized that REST interfaces make life much easier. (also see here) As a result, a number of these services have simple REST interfaces. One such service provides molecular descriptor calculations, using the […]
The Speedups Keep on Coming
A while back I wrote about some updates I had made to the CDK fingerprinting code to improve performance. Recently Egon and Jonathan Alvarsson (Uppsala) had made even more improvements. Some of them are simple fixes (making a String[] final, using Set rather than List) while others are more significant (efficient caching of paths). In […]
Conformational Envelopes
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 […]
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 […]