Secondary Structures from 3-D coordinates

Steven Brenner seb1005 at mbfs.bio.cam.ac.uk
Thu Sep 23 05:32:43 EST 1993


gjb at bioch.ox.ac.uk (Geoff Barton) writes:
>You need DSSP from Chris Sander at EMBL.  I think the program is available
>on the EMBL file server.

>See the paper:  Kabsch and Sander (1983) Biopolymers, 22, 2577-2637

DSSP will nominally provide the desired output, but its assignments of
secondary structure frequently disagree with those of those who solved
the structure.  There are many reasons for this (many of them not
DSSP's fault), but mainly it appears to be a consequence of DSSPs
simple algorithm for determining secondary structure.  

Therefore, it may also be worth looking at VADAR, which performs the
same task using somewhat more sophisticated criteria.  The program was
developed by David Wishart at U Alberta.

The program can be found at canopus.biochem.ualberta.ca as
  pub/VadarAug93.tar.Z

Steven

P.S. DSSP may be found on ftp.embl-heidelberg.de in the directory
  pub/databases/protein_extras/dssp.   Source code is available by
signing the license agreement; executables are found in that directory.
-- 
Steven E. Brenner               |  Department of Biochemistry      
seb1005 at mbfs.bio.cam.ac.uk      |  University of Cambridge         
Lab   +44 223 333671            |  Tennis Court Road              
Fax   +44 223 333345            |  Cambridge CB2 1QW, UK          



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