On 10/21/2017 01:58 AM, Andy Jennings wrote:
Hi,
I'm curious if anyone has figured out a way to compare two molecules
based upon their pharmacophore similarities. Specifically, I want to
compare 2 molecules in their _absolute_ locations, and not simply see if
they have 2 pharmacophores that match well via a translation/rotation.
From what I can see in the RDKit code the current implementation,
whilst excellent, is limited to distance matrices and not absolute
coordinates.
My use-case is where I have aligned 2 molecules in some fashion and then
want to compare how similar their electrostatic surfaces/pharmacophores
are in that specific relative orientation. Think 'R0CS' color for RDKit,
if that helps. I appreciate that thinking about bringing more 3D
functionality to a cheminformatics toolkit may be heresy, but I'll run
that risk.
There is an open source tool called Pharao.
I guess it can do some scoring of two already placed molecules in 3D in
the pharmacophore features space.
I also want more 3D in rdkit (like surfacing of atoms with controllable
atomic radii); many people work with structural data.
My current nasty hack is to locate all pharmacophores in query/reference
molecules, assign coordinates and orientation to them, and loop over any
pharmacophoric patterns that both molecules contain.
Thanks in advance,
Andy
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