12 June 2013

What you are Missing.

The nice part about blogging is you can post anything you want.  Mostly, we post on interesting (to us at least) papers, news about fragments, conferences, and so on.  We have assiduously avoided being a commercial outfit; what we post is what we believe in and we don't post for cash or barter.  So, we tend to not promote people/companies.  I am so totally breaking that rule right now.  

Many of you probably know Chris Swain, the principal of Cambridge MedChem Consulting.  [Full Disclosure: Chris and I have worked and published together.  I hope that does not diminish your feelings about him.  :-)] If not, this post will introduce you to him and the many wonderful resources he curates, particularly in the FBHG world.  There is so much there, sometimes I forget what he has; in fact, Chris's site goes by the rule, "Why make them buy the milk, give it to them, and the cow too!"  

One of the great resources Chris has is a graphical snapshots of a metric pile of fragment collections.  On Monday, Chris added nPMI (Principal Moment of Inertia) to these snapshots.  As has been discussed some, I (and Justin Bower from the Beatson) think this is the best way to evaluate "3D-arity".  It is interesting to just browse through the snapshots.  Some of the collections that are VERY large do seem to have a good to excellent amount of 3D-arity.  Does this correlate with increased hit rates for certain target classes?  

Well, Chris has thought of that.  He has been collecting the compounds from the literature that are reported as fragment hits.  He has just updated that snapshot with nPMI also.  What do the reported fragment hits tell us?  I would say that the vast majority of the reported fragments are Voldemort Rule compliant.  No surprising.  What I would like to see is a breakdown of fragment property against target type.  This may the part of the cow Chris isn't giving away.  There may be other slices/dices too.  

Trust me, go and spend some time on Chris site.   I won't call it a time waster, but it will suck you in.


Chris Swain said...

Thanks for the kind comments, and yes I plan to compare targets. I've more records to add and I've spoken to the people at ChEMBL about copying their ontology, once done I'll do the analysis

Dr. Teddy Z said...

And hello to our spammer.