Version 1.0.5 of the CDK descriptor calculator is now available. This version updates the command line batch mode to allow one to calculate a specific set of descriptors (as opposed to all or say, topological). The selected descriptors are specified using an XML file, which can be generated in the GUI mode – fire up […]
Update to the fingerprint Package
I’ve just uploaded a new version of the fingerprint package (v3.3) to CRAN that implements some ideas described in Nisius and Bajorath. First, the balance method generates “balanced code” fingerprints, which given an input fingerprint of N bits, returns a new fingerprint of 2N bits, such that the bit density is exactly 50%. Second, bit.importance […]
Some More Comparisons with the GSK Dataset
My previous post did a quick comparison of the GSK anti-malarial screening dataset with a virtual library of Ugi products. That comparison was based on the PubChem fingerprints and indicated a broad degree of overlap. I was also interested in looking at the overlap in other feature spaces. The simplest way to do this is […]
A Quick Look at the GSK Malaria Dataset
A few days ago, GSK released an approximately 13,000 member compound library (using the CC0 license) that had been tested for activity against P. falciparum. The structures and data have been deposited into ChEMBL and a paper is available, that describes the screening project and results. Following this announcement there was a thread on FriendFeed, where […]
New Version of rcdk
Based on feedback from the recent R workshop at the EBI, I’ve updated the rcdk package to include more methods operating on atoms, a modification to parse.smiles to allow it to handle a vector of SMILES strings, which makes it more R-like (thanks to Tobias Verbeke for the patch). In addition, one can now load […]