With the recent stable release of the CDK (1.3.12) and the inclusion of the new rendering classes, I was able to make a new release of the rcdk (3.1.1) and rcdklibs (1.3.11) packages that support cheminformatics in R. They’ve been pushed to CRAN and should be visible in a day or two. The new features […]
The CDK Volume Descriptor
Sometime back Egon implemented a simple group contribution based volume calculator and it made its way into the stable branch (1.4.x) today. As a result I put out a new version of the CDKDescUI which includes a descriptor that wraps the new volume calculator as well as the hybridization fingerprinter that Egon also implemented recently. […]
Accessing High Content Data from R
Over the last few months I’ve been getting involved in the informatics & data mining aspects of high content screening. While I haven’t gotten into image analysis itself (there’s a ton of good code and tools already out there), I’ve been focusing on managing image data and meta-data and asking interesting questions of the voluminuous, […]
Call for Papers: High Content Screening: Exploring Relationships Between Small Molecules and Phenotypic Results
242nd ACS National Meeting Denver, Aug 28 – Sept 1, 2011 CINF Division Dear Colleagues, we are organizing an ACS symposium, focusing on the use of High Content Screening (HCS) for small molecule applications. High content screens, while resource intensive, are capable of providing a detailed view of the phenotypic effects of small molecules. Traditional […]
CDK & logP Values
Recently, Tony Williams enquired whether there had been any comparisons of the CDK with other tools for the calculation of polar surface area (PSA) and logP. Given that PSA calculations using the fragments defined by Ertl et al are pretty straightforward, it’s not surprising that the CDK implementation matches very well with the ACD Labs […]