A number of things came into conjunction recently that inspired me to embark on my first WikiGenes edit, including the fact it was now being included as a cross-reference in key resources such as Wikipedia, HGNC and iHOP (maybe UniProt next ?). I have no inclination to check and/or contribute to all the protein records I have had some engagement with, but the choice for my first effort was LACTB .
Updates Sep 20, 2013 Two new codes added, thanks to spots by commenters (see botom of post) Unmapped code names have been appended to the end of this post for crowdsourcing, a subsequenct post has addded in the AZ/MRC compound list and we now have a paper out on the combined results.
This post follows-on from Suddenly-its-raining-patent-chemistry and Med-chem-letters-patent-highlights . As additional context I am pleased to declare that I have recently been appointed as a member of the SureChem Advisory Board.
I've been a long time fan of InterPro and even managed to pen a review of its early incarnation. While I have also been impressed by InterProScan, like most users I suspect, I simply assumed the results for Signal peptides and C-terminal transmembrane domains were generated on the fly by SignalP and TMHMM as part of the scan run. However, from using it over some time on a large set of
1) Yesterday, Twitter came up with the ”similar to (me)" suggestion of one of the ACS accounts. I took a look and was suitably intrigued by the new patent reviews. 2) I noted the essential details, including some IC50 mapping, had been distilled by the review author (Fatty Acid Synthase Inhibitors as Possible Treatment for Cancer) and summarised in the open PDF (no pay-wall to bust) 3)
This is a continuation of the fishy-bace1-and-bace2-story and geting-your-kicks-on-ensembl-66 but I shall now amble further down the phylogenetic tree to the lowly creature pictured below that goes by the name of Ciona intestinalis a.k.a. the Sea Squirt. Ascidians are Urochordata decended from the ancestor of all chordates at least 520 million years ago.
We all know that nagging feeling "there are powerful utilities here but I just need to spend some time sussing them out...." In this post I'll run through some of what I explored in MyNCBI, with particular reference to PubChem. I had used stored searches for some years back at the Elk ranch and at the EBI but I recently needed to exploit this deeper to apply it to consultancy work and collaborations.
(See update at end of post) As we know Google is a well established chemistry search tool but I have noticed patchy coverage (see will-real-bosinhib-please-stand-up). I decided to perform the experiment of putting these text strings up at 12:18 today, when the InChI key had just one hit
This a sequel, and a wrap-up for me at least, for the post Shop Till You Hit: Chemical Suppliers and Malaria OSDD so you will need to take a quick look at that for this to make sense. The questionnaire, (still open, if there are chemical vendors who missed it) despite some helpful re-tweeting, collected a mere two replies, the contact details for which have be forwarded to the Sydney group.
24 of August: There is now a follow-up post; NCATS repurposing compounds in PubChem: Part II with an expanded list of 33 structures. 29 July: there are some updates, comments, and new IDs described at the bottom of this post. The final small-molecule total resolved to CIDs is now 30 out of 56. Checking has revealed source ambiguity for one record.
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.