Drug informatics can seem somewhat abstract until it translates to direct experience. Spending ~ 20 hours zonked out with a bacterial infection and hoping that the antibiotics were the right stuff to enable you to recover, forcibly brings this home. This was my second encounter with septicemia the first being some years ago, starting from a skin pimple, that laid me out for several days and needed antibiotic switches.
Update Monday 11th June I have merged a couple of aspects recently explored for chemicalize.org because they retro-fit to the short UGM report below. Two things happened last week. The first, after finding Google docs somewhat quirky for shared editing I was doing, was a test of Dropbox as an alternative.
Update 8th Sep. This subject has just come up on the ChEMBL blog The latest installment of this story popped into my Twitter feed this morning as the How-many-varieties-of-bosutinib-made-it-to-public-domain-databases ChemConnector (AW) post with a set of links on the story so far.
I was not only fortunate to be invited to the 10th anniversary BioIT World in Boston this April but also chuffed to get my second “triple-decker” badge, shown below on the right, with the first one from 2009 on the left. However, I can confess to making a last-minute pitch for that third ribbon!
Updates 14th May and 27 July, mainly corrections related to comments (with thanks). Also, please see sequel post shop-till-you-hit-part-II. ***************************************************** I am pleased to be participating in the OSDD antimalarial project (AMP) in a small way and have been following the interesting implications for open drug discovery for major tropical diseases.
This "chem-plus-bio" post arises from the propitious conjunction of the release of SureChemOpen and the recently declared new drug target status of BACE2 (Q9Y5Z0). We can start with the biology first. My historical engagement with BACE1 (P56817) as a drug target for Alzheimer's disease and abiding interest in the evolutionary history of the enzyme has been mentioned in previous posts.
I have just reached an arcane but personally significant landmark in that, as result of an update request by me at the end of 2011, the last of my UniProtKB /TrEMBL entries has been subsumed into Swiss-Prot. I take some pride in the fact that my name, along with those of my co-authors or co-submitters, is consequently indexed in 32 UniProt “reviewed” entries, up from 31 + 1 TrEMBL previously.
Its not every day I get quoted in Nature News so this definitely merits a post. By the nature (no pun intended) of these summaries they don’t leave much room for context so I can take this opportunity to add some. I enjoyed the interview and the piece provides a useful snapshot, certainly as judged by multiple Tweets. However, I should start by setting the record straight (not that it was really that bent)
A lot of interesting things have come up via the #ACSSanDiego Tweet tag but my attention was particularly grabbed by live blogging the first disclosures of drug structures by @carmendrahl linked to hand-sketches of these in her blog post. This had resonance with me from an (AstraZeneca internal) Yammer post of mine last year.
These have been introduced and cogitated upon in a number of places, including the usual NRDD 2011 FDA drug approvals article. Here I will include links from the ChEMBL Blog that have useful contextual information including target mappings.
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”.