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Bio <-> Chem

Technical notes from the interface between bioinformatics and cheminformatics by Chris Southan
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Drug ApprovalsBiologieEnglisch
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Autor Christopher Southan

Update : 2nd Feb, a statistical review from C&ENews (n.b. Blogger is loosing some of the link highlighting later in the post, but, via mouse-over, you can get out to them). This is an annual follow-on from previous years (e.g.2014,  2013 and 2012). Adding the 45 NMEs and the  biologicals comes to 51. Good news for a good year then but I shall link to the pundit commentaries as they surface.

Clinical TrialsBiologieEnglisch
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Autor Christopher Southan

I freely admit my response to this tweet was too hasty; However, the knee-jerk had an explanation since I had just been collating a post about integrated bioactivity databases.  Considering there are already 17 of these (and probably more on the way) we are, in the community sense, heading towards overkill and paralysis of choice.

BioactivityDatabasesBiologieEnglisch
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Autor Christopher Southan

Update : April 2016 links added in the post 1) CTTV re-branded as as Open Targets 2) New link to assessment of GotPdb in-links 3) New PAROS source for NIH druggable genome ******************************************************** As some of you may have picked up from social media we were pleased to make it into the NAR 2016 Database Issue

Drug StructuresBiologieEnglisch
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Autor Christopher Southan

So how many "drugs" are there? (in the pharmacological context of approved medicines). Its actually a surprisingly difficult question to answer.  I am in the midst of drafting a manuscript to address the subject  primarily at the structural comparison level using sources I can either extract from,  or map into, PubChem and therby explicitly count and intersect them as CIDs.

KinasesPubChemBiologieEnglisch
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Autor Christopher Southan

This post will resolve molecular links to two recent kinase papers. I will address the one from July  " FDA-approved small-molecule kinase inhibitors " (PMID 25975227) as the second, since it has a smaller molecule set. The newest of the pair is " Comprehensive characterisation of the Published Kinase Inhibitor Set " ( Nat.

ChemIDPlusDrug ApprovalsDrug StructuresFDA/SPLBiologieEnglisch
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Autor Christopher Southan

As well as laying out what I hope are useful observations, this is also a call  for filling in knowledge gaps (please) on the information labyrinth associated with the surfacing of  newly approved drug structures. The main reasons are a) its an important part of what we do at GtoPdb  b) it could add context for a nascent manuscript broadly based on this  ACS presentation

Chemistry LinkingInChIKeyMark-upBiologieEnglisch
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Autor Christopher Southan

Update: July 2016.  We have a blog post over on the ranch page as Hot topics: linking chemistry to papers which introduces the paper below (PMID 27293485) wherein GtoPdb gets an honorable mention and chemistry-to-PMID linkage statistics.

MK-8931VerubecestatBiologieEnglisch
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Autor Christopher Southan

Update: 02 Nov 2016.  The good news for BACE1 inhibitors in general and Merck in particular is that the Phase II trial results just published for verubecestat look encouraging. Note also what could be a double stroke of good fortune if this tweet is substantiated.