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

I continue to have a lot to do with this big theme.  It is not only the subject of our 2011 paper but I also have a slide set used this April/May for a presentation to the PubChem team,  a BioIT World chemogenomics workshop and the ChEMBL users group meeting.  I’ll point to these slides so as not to reiterate but will go through some new examples in more detail.

If you don’t know that  much about the IPI  you will need to get the gist of it or this post, offering  arguments for  not closing it down, will be a bit challenging.  I first looked this database when I was writing a review on protein number  in 2003 and had numerous chats with PK about it over the phone.

As well as the usual annual Nature Drug Discovery article you can find background information in the ChEMBL blog including target mappings so I shall just make a few observations related to the PubChem links per se. These are presented as an alphabetic INN listing (and one trade name) of the 2010 approvals that mapped, as best as I could ascertain, to CIDs 1. Alcaftadine (Lastacaft) = CID: 19371515.

We expect databases to show growth but there are occasions when, just for  a change, they shrink.  This is the story behind a big dip in PubChem compounds that you can see in this slide from SB's presentation at TACBAC in March 2010. The story starts about a week before the end of July 2009 (but my blog doesn’t go back that far)     1)

Subsequent to my  2004  publication and a presentation at the Swiss-Prot 2006 conference I maintain  an abiding interest in what, at that time, I  termed the basal (i.e. unspliced) protein number.  In deference to the Swiss-Prot philosophy and curation rules I would now term this the “canonical” number of primary ORFs to which sequence variants from gene loci would be mapped.

It can be difficult to retro-fit a readable narrative to a story but this started when, as part of the day job,  I was following a few well established drugs through some internal applications I was documenting last year. This included following the public outlinks for synonym and cross-mapping checks.  Unsurprisingly, considering this was AZ Mölndal,  one of these was Crestor.

Since therapeutic antibodies are the new pharma rock and roll (not to mention pipeline stuffing) I decided to see what I could find from the 2009 approvals in the same listings that supplied the small-molecule drugs in the previous post. In particular I wanted to track down the exact protein sequences. Why ? in the first instance simply because this was a challenge.

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