README for zinc8.docking.org/filtered/
Dec 18, 2008
support at docking.org

This directory contains compounds filtered out of supplier catalogs and not loaded 
into ZINC. Note, the filtering rules continue to evolve, so the same rules have not 
been applied uniformly. Our general rule is to load any molecule that is commercially
available and could plausibly

a) bind specifically and non-covalently to a protein, 
b) be sufficiently soluble under typical assay conditions,
c) be stable under typical assay conditions and
d) be free of pathologies for typical docking software.

We tend to exclude compounds that 

i) are big  (opinion varies from 400 to 600 Da as a pragmatic cap)
ii) are floppy (opinion varies from 7 to 12 rotatable bonds as a pragmatic cap)
iii) have too few or too many polar atoms
iv) have features that cause assay artifacts

It is this last item that is most open to interpretation, and for this reason, 
we offer a "clean" version of each of our subsets.