>Subject: Secondary Structures from 3-D coordinates
>Date: 21 Sep 93 03:20:26 GMT
>Sender: daemon at net.bio.net
>Does anyone know of a program that takes 3-D coordinates of a protein,
>interprets secondary structures present, and outputs a linear secondary
>structure assignment underneath the primary sequence ?
>I would like to be able to compare predicted secondary structures (e.g.
>PredProtein server) with known secondary structure(s) of other protein(s)
>in a given family.
>Roger Graham
>UBC Microbiology Vancouver flo at unixg.ubc.ca
In reply to the query in article 822 I would refer you to the
Kabsch and Sander algorithm as described in Biopolymers (1983)
22, 2577-2637. The program is well described here and is supposedly
available from the Brookhaven PDB. I have heard there are problems
with the program as available from Brookhaven but I have no personal
experience with it.
I obtained a program written in C based on the above mentioned
algorithm from Mike Carson at UAB's macromolecular crystallography
group. I do not know if it is generally availble but I know that it
works. You can reach Mike at carson at luna.cmc.uab.edu, and hopefully he
will reply.
Good luck,
Vince waterhous
Biophysics, Oregon State University
waterhod at bcc.orst.edu
