If you are interested in finding other interactions that look like one
particular one, rather than just classifying things (e.g., "is this
cyan, sea-foam, turquoise or teal?"), then I'd recommend the
substructure searching capabilities of the DrugSite server
You can specify any arbitrary segments of an existing structure (by
residue ranges, small or large) and find all other structures that
have the same backbone geometry.
If the target residue segments are from different molecules in a known
complex, it will find similar complexes.
The server returns coordinates overlaid using only the residues in
your defined target.
https://drugsite.msi.umn.edu/
Barry C. Finzel
Medicinal Chemistry Department
University of Minnesota
finze...@umn.edu
On Oct 28, 2013, at 1:23 PM, Katherine Sippel wrote:
Hi all,
I was wondering if anyone knew of a software or server to mine the
PDB for a specific class of interactions? I've tried PDBeMotif
without much luck and I thought I'd check to see if there was an
alternative before I go re-inventing the wheel.
Cheers,
Katherine
--
"Nil illegitimo carborundum" - Didactylos