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 […]
Working With Fingerprints in R (can’t beat C!)
Since I do a lot of cheminformatics work in R, I’ve created various functions and packages that make life easier for me as do my modeling and analysis. Most of them are for private consumption. However, I’ve released a few of them to CRAN since they seem to be generally useful. One of them is […]
AJAX’ified Pub3D
Pub3D is a 3D version of PubChem, in which we have generated a single conformer for 99% of PubChem using the smi23d suite of programs. The structures are then stored in a PostgreSQL database along with their distance moment shape descriptors described by Ballester and Graham-Richards. This allows us to perform shape similarity queries against […]
Moving to SlideShare
Finally got round to putting a number of my slides onto SlideShare. While I was skeptical initially, I’ve found it quite handy to quickly browse through a presentation without having to download PDF’s or PPT’s and start up the viewers. Also this lets me not have to maintain a webpage listing all the presentations I’ve […]
CDL – A Cheminformatics Toolkit
The Chemical Descriptors Library (CDL) has been around for a while, but hasn’t seemed to get much publicity. A paper describing the design and performance of the library just came out today. While the name suggests a library of descriptors, it’s actually a general C++ library for cheminformatics. The library appears to use the molecular […]