Cryptography & Chemical Structure Search

Encryption of chemical information has not been a very common topic in cheminformatics. There was an ACS symposium in 2005 (summary) that had a number of presentations on the topic of “safe exchange” of chemical information – i.e., exchanging information on chemical structures without sharing the structures themselves. The common thread running through many presentations was to […]

Retrieving Target Classifications from ChEMBL

There are a number of scenarios when it’s useful to be able to classify protein targets – high level summaries, enrichment calculations and so on. There are a variety of protein classification schemes out there such as PANTHER, SCOP and InterPro. These schemes are based on domains and other structural features. ChEMBL provides it’s own […]

Words, Sentences, Fragments & Molecules

For some time I have been thinking of the analogy between linguistics (and text mining of language data) and chemistry, specifically from the point of view of fragments (though, the relationship between the two fields is actually quite long and deep, since many techniques from IR have been employed in cheminformatics). For example, atoms and […]

SALI in Bulk

Sometime back John Van Drie and I had developed the Structure Activity Landscape Index (SALI), which is a way to quantify activity cliffs – pairs of compounds which are structurally very similar but have significantly different activities. In preparation for a talk on SALI at the Boston ACS, I was looking for SAR datasets that […]