3D fragments is still a topic up for discussion/debate. Of course, determining what is a 3D fragment is also open to debate. As presented last year, nPMI seems to be the current "best" method. FOB Chris Swain has done some neat analyses around nPMI and included it in his overview of commercial libraries. Last year at the NovAliX Biophysics conference, Glyn Williams from Astex presented the "plane of best fit" (PBF) as a superior way to analyze 3D-arity. At the recent Zing FBDD conference, Chris Murray presented the "plane of best fit" and argued again that it was superior. So, of course, I asked Chris Swain if he had compared them, and he said, but wait a minute.
Well, Chris was able to compile it with the help of his son, Matt (obviously the apple does not fall from the tree). So, go check out his comparison of nPMI with PBF. He ran 1000 fragments through both and concluded this:
Whilst both descriptors are intended to provide information on the 3D structure of the molecule it looks like the PBF provides more granularity which may be particularly useful when looking at small fragments.
So, I present this as a "go get 'em, folks!". I am particularly interested to know if people are currently using PBF and if their results jibe with Matt's.