[Q] secondary structure from coordinates

Andrew Dalke dalke at uxa.cso.uiuc.edu
Sun Nov 27 08:38:00 EST 1994

  I'm working on finding the secondary structure of an protein (helix,
sheet, etc.)  given the atom coordinates.  I've already written the
routines to read a PDB file and determine the connectivity, so the
hard part is written.  I just can't figure out how to do it on my own.
  I've come up with two ideas; either look at the phi/psi angles on a
Ramachandran plot, or determine some of hydrogen bonds.  Now I know
this is something which has been done half a hundred times before, and
I don't completely want to reinvent the wheel, so if someone could
give me some pointers to a standard reference, or could tell me how
most people to this, I'll be rather thankful.

  As long as I'm at it, ... I also want to figure out which, if any of
the DNA bases in the structure are paired.  Is this another problem
that should be solved by looking at the possible hydrogen bonds
between the ends of the bases?

  Thanks in advance,

						dalke at ks.uiuc.edu

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