[Q] secondary structure from coordinates

gjacobs at chmeds.ac.nz gjacobs at chmeds.ac.nz
Sun Nov 27 16:17:29 EST 1994


In article <3ba23o$atq at vixen.cso.uiuc.edu>, dalke at uxa.cso.uiuc.edu (Andrew Dalke) writes:
>   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.

I presume your problem is not working out the phi/psi angles, but what
range of values ought to be a helix, etc.? Maybe look up the ref. for
PSSB (hope I've got the name right) - it ought to be by Chris Sander's
group and see what they use. Reading it again, you sound a little
confused: the usual thing is to just use the torsion angles as they do
in PSSB. I'd be suprised if PDB don't supply a program to do this -
the PDB or EMBL email/ftp servers...?

>   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?
> 
  H-bonds would seem the thing, but also the planarity of the bases:
sometimes not all H-bonds are formed (due to propeller twist, etc, etc).

Food for thought, I hope, anyhow.

Grant Jacobs



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