[Q] secondary structure from coordinates

Andrew Dalke dalke at uxa.cso.uiuc.edu
Mon Nov 28 00:48:32 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.
>> ...

To which Grant Jacobs <gjacobs at chmeds.ac.nz> replied
>I presume your problem is not working out the phi/psi angles, but what
>range of values ought to be a helix, etc.?

  Absolutely correct.  Finding the angles are easy; classifying them
is harder.

>                                            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. 

  I looked around on archie and some of the www searchers and couldn't
find a reference to PSSB.  Could you point me out where to look?

>       I'd be suprised if PDB don't supply a program to do this -
>the PDB or EMBL email/ftp servers...?

  I looked in both of those FTP servers and couldn't find anything.
The closest was the "dihdrl" program at the pdb which will find the
psi/phi/etc angles.


  What I would like is a list saying something like:
psi between X1 and Y1  &  phi between A1 and B1  =>  helix
psi between X2 and Y2  &  phi between A2 and B2  =>  helix
psi between X3 and Y3  &  phi between A3 and B3  =>  beta sheet
...

						Andrew
						dalke at ks.uiuc.edu



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