“Type-ahead” substructure searches

The other day I was exchanging emails with John Van Drie regarding open challenges in cheminformatics (which I’ll say more about later). One of his comments concerned the slow speed of chemical searches Google searches are screamingly fast, so fast that the type-ahead feature is doing the search as you key characters in.  Why are all chemical […]

Substructure Searches – High Speed, Large Scale

My NCTT colleague, Trung Nguyen, recently announced a prototype chemical substructure search system based on fingerprint pre-screening and an efficient in-memory indexing scheme. I won’t go into the detail of the underlying pre-screen and indexing methodology (though the sources are available here). He’s provided a web interface allowing one to draw in substructure queries or […]

PAINS Substructure Filters as SMARTS

Sometime back Baell et al published an interesting paper describing a set of substructure filters to identify compounds that are promiscuous in high throughput biochemical screens. They termed these compounds Pan Assay Interference Compounds or PAINS. There are a variety of functional groups that are known to be problematic in HTS assays. The reasons for […]

Substructure Matching, REST style

I’ve been putting up a number of REST services for a variety of cheminformatics tasks. One that was missing was substructure searching. In many scenarios it’s useful to be able to check whether a target molecule contains a query substructure or not. This can now be done by visiting URL’s of the form 1http://rguha.ath.cx/~rguha/cicc/rest/substruct/TARGET/QUERY where […]