Q: Secondary Structure Designations

Julianne M. Braun braunjm4 at wfu.edu
Mon Jul 27 15:01:26 EST 1998

Is there a standard method for designating primary and secondary
structure of proteins?  I'm familiar with mixed case three letter
abbreviations delimited by dashes or hyphens (e.g. Pro-Ala-Gly) and with
one letter abbreviations (e.g. PAG) for primary structure, but if one
also wants to designate known secondary structure how would that be
done?  Are secondary structure designators placed between residues in
the same string of text?  Is it more common to list out the residue
range that has a certain structure?  If a list is common, would it
normally include designation of secondary structure for all residues or
just for those of known structure types (i.e. random coil residues would
be left off the list)?  Is it common at all to see secondary structure
for all or part of a protein published in the absence of tertiary
structure determined by X-ray?

I've been working with ACD Labs software ChemBasic & ChemSketch (free
from http://www.acdlabs.com) writing some software that accepts input of
amino acid primary and secondary structure and prepares 3-dimensional
molecular structures that can be saved as *.MOL or *.VRML files.  (3-d
structure can be saved based on just the secondary structure, wtih
side-chains oriented relative to the backbone as they are in the energy
minimized conformations of unassociated amino acids, or a conformation
analysis can be performed to energy minimize the entire protein
structure.)  I'd like to make the input as user friendly as possible by
using standard formats for the input.  It would be nice if a sequence
from a publication could just be cut and pasted into the program.

Any information gratefully received!

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