Cultural reference prelude:  Many of you may know the Rolling Stones rendition of  (get your kicks on)  Route 66  but I chose the Chuck Berry and Manhattan Transfer versions for my MP3 collection.   Ensembl is fantastic for many reasons.  It is also a clean retrieval tag so we can count over 7 million specific Google hits, which goes up to  437 million if you just add the “e”.

In the last few days PubChem has a new source that merited a newsflash and has bumped the IBM patent structures  off the top slot.  While this is a new entrant into the PubChem fold TTD per se is well established and their recent update is published (PMID 21948793).  I can take a micro-credit for encouraging this to happen via my contacts with both sides, although the respective teams did all the real work of

(Update: 24 Feb. It was nice to get a mail response from Zfin the Zebrafish database so we'll see what ensues) As part of a rather long manuscript gestation I keep an eye out for new sequences relevant to the evolution of BACE1 and BACE2.   You can see the bare bones of the story up to 2009 in this poster from JH and  myself .

New sources and tools, both public and commercial, for the automated extraction of chemical structures from patents, now termed Chemical Named Entity Recognition (CNER), are being declared with increasing frequency. I’ve pointed to some of the public ones in a previous post  and our recent paper (Sorel et al 2011) includes a comparison between commercial large-scale automated and manual curation sources for patent chemistry (see fig.

The first part of this story is - sort of - our fault.  Once upon a time, we wuz digging novel human proteases out of EST data and filing patents as fast as we could clone ‘em  (which wasn’t that fast in fact).  One of these happened to be homologue of a bacterial serine beta lactamase so we duly filed it as WO9957286 but, because it did not look like the next big drug project target we were permitted to publish.

This post is the result of a  conjunction between two events The first was that chemicalize.org came up in the LinkedIN Cheminformatics group just recently so I  decided to give it a re-spin having been impressed with earlier versions.  The second was the announcement last week of WIPO Re:Search. So I've combined trying them both out, synergistically you might say. WipoRe:Search is a

Well,  I  had my 50th Party at the White Swan Pub in Twickenham (pictured below), which was  nice but actually some time ago, ‘nuff said.   However, what happened more recently, at the beginning of this September,  was the appearance of my 50th entry in PubMed  which was our “Minimum information about a bioactive entity (MIABE)”

This list of  July USANs has been copied over (with thanks) from the ChEMBL blog to follow up a few things.  I chose it because as small list I could quickly do three things 1) an (exact match) Google count of the name,  2) the same with the research code and 3) a PubChem mapping either by a name hit or scraping the IUPAC out of the PDF, pasting in to OPSIN and then pasting the SMILES into the PubChem search box.

This lady, a woodland Gorilla called Kamilah, has had her genome sequenced by the Sanger Centre and just undergone an updated Ensembl release. You can inspect her BACE1 gene via the Ensembl Compara GeneTree  display  (not to be confused with TreeFam or TreeView )

Looking at the  DrugBank collection of DPPIV inhibitors for a previous post involved checking  the three approved  “gliptins”. This relatively new class of protease inhibitor drugs for diabetes seem to be crossing or coming up to the FDA finish line thick and fast (altought it is ranked 25th of all research targets by compound numbers )  I was therefore

I’d like to make a few comments on what might be one of the most significant bioinformatics papers for drug R&D in a long time “Testing the Orthologue Conjecture with Comparative Functional Genomic Data from Mammals” . It has implications for the interpretation of drug effects in animal models or cell systems that echo all the way up from pharmacological proof of concept to safety assessment and the productivity crisis associated with