Filtering rules in effect at docking.org
For each set of filtering rules, we provide them in raw text and also in an
graphic form. Thanks to Mattias Rarey and his group for
SMARTSviewer.
Basic filters: applied to all vendor catalogs
Annotated catalog filters
Catalogs of biologically active molecules
are filtered using more permissive rules (because they are active).
Secondary filters
Molecules are annotated as potentially problematic if they match any of
these filters.
yuck rules
The "clean" subsets in ZINC have any molecule matching any of these two
yuck rule sets filtered out.
Editorial comment: We do not endorse either set of yuck rules.
They are provided merely as a convenience to users.
Many perfectly good actives and over 1/2 of purchasable chemistry
are filtered out by these rules. caveat emptor
yuck1 rules
A second set of rules.
Blaster rules
During upload and DOCK Blaster, we are more tolerant of ligands since they
bind (i.e. in the PDB).
These are like the rules for
Many thanks to David M. Lorber for the filtering script
and our colleagues for advice.
As always at docking.org, the sole responsibility
for any errors is John Irwin's.
Finally, a wide range of SMARTS definitions.
Last updated: October 2011.