[Dock-fans] use_clash_overlap and use_internal_energy
jmp17 at duke.edu
Wed Jun 11 14:37:40 PDT 2008
We have been using anchor-and-grow to perform flexible docking and
minimization on a large number of compounds from the zinc7 database. Many
of the highest scoring compounds suffer from geometries with unreasonable,
overlapping functional groups and rings. I really don't think we can trust
the results we've obtained thus far.
Our goal is to generate leads via docking, then synthesize approximately
20-50 molecules and assay them to determine if they are in fact
I have seen previous posts regarding "interpenetrated" structures, etc.,
but I'm still not sure how to circumvent this problem. It seems to me that
use_internal_energy should prevent these types of overlaps if the
repulsive vdw exponent is in effect. Any help/advice would be appreciated.
I have attached a representative input file below.
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