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.
Barry C. Finzel
Medicinal Chemistry Department
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
