[**Programming Note** Sorry about two posts in one day, but I thought this was too cool to wait.]
The 3D-arity of fragments is a common topic of discussion in this field. ICYMI, Chris recently did an analysis of PPI interactions and the compounds that target them. However, even more recently, Chris just put up his analysis of the 3DFrag consortium's fragment collection. The 3DFrag collection does not look any more 3D than commercially available collections. Justin Bower from the Beatson points out that this is because their fragment collection is largely due to culling from commercial collections.
Now, no one will argue that nPMI is the best metric for assessing 3D-arity. But it is the best we have so far. So, Chris has tried to improve on the visualization of nPMI for very large libraries. Chris has divided the PMI plot into regions that are disc, rod-like, or spheres (he details how he classifies them at his page). The upshot of this is that he can then generate very simple plots like this:
I think this is a great leap forward. Obviously, because of the nature of the chemistry performed over the past umpteen years, this would be totally expected. As Peter Kenny has pointed out previously, rods have volume, but I think that is not what the 3D-eers are aiming at. What's really nice is that 3DFrag has chemists to make fragments. In May, they reported that they had added 221 synthesized fragments. I would like to see how these 221 fragment differ from the commercially available ones. The proof is always in the pudding after all.