Subject: Peptide-Database

From: [email-masked]
Date: Tue, 13 Nov 2001 15:19:20 +0100

Hi CCLers,
          obviously it's not perfectly
trivial to automatically  scan the PDB for
peptides or peptide-like drug molecules.
Thus, I am just trying to compile some sub-
databank of peptide structures.
          With peptides very often being a
sequence including both atom and heteroatom-
entries, resorting to SEQRES - information seems
the only thing that really works. Coordinates are
seemingly not accurate enough to determine molecular
connectivity based on proximity of atom positions alone.
Yet, in 1nqr one chain actually includes two molecules,
thus connectivity SEQRES on its own is obviously non-
sufficient as well. For the moment I will try to use SEQRES
records and check connectivity by measuring atomic distances
of neighbouring residues.
          Is anybody aware of any
existing databases of that kind? Any suggestions
and comments of how to compile such a data-
base are also welcome.

Cheers,

Maria