Secondary Structures... Summary

gilkes at unixg.ubc.ca gilkes at unixg.ubc.ca
Mon Sep 27 20:17:46 EST 1993


Q. 

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.

	Thanks to all who send replies to this query.  Suggestions follow :

1. Both the GCG (Genetics Computer Group) sequence analysis suite of
programs, and the PSA (Protein Sequence Analysis) package by Gary Gilliland
and James Jenson will output that style of data from a Chou-Fasman
prediction, and GCG will also give you GOR style predictions as well.	Brian
W. Beck     brian at bert.chem.wsu.edu  

2. Molecular Simulation's QUANTA will do this for you under its "protein
design"
menus. It will display a rotatable alpha carbon backbone in colours
corresponding to secondary structural elements and displays the primary
sequence in appropriate colours above the structure.	Orhan W.D.
Ertughrul	e-mail : owde100 at cus.cam.ac.uk

3. Try DSSP written by, I think Kabsch/Sander. For more information
look: 
  Dictionary of Protein Secondary Structure: Pattern Recognition of
Hydrogen-Bonded and Geometrical Features. Wolfgang KABSCH and Chris SANDER
(1983), Biopolymers
Vol. 22, 2577-2637.  In the paper they explain how they recognize secondary
structure based on combinations of bond angles, H-bonding etc. The program
is available at the anonymous ftp-server at EMBL-Heidelberg. Ready to run
versions for various machine-types can be found in /pub/software/unix/dssp
(SGI, SUN, EVS, DEC, VMS).  Source code is available by signing the license
agreement; executables are found in in the directory
pub/databases/protein_extras/dssp. The program is also available from Chris
Sander (e-mail: Sander at EMBL-Heidelberg.DE)  Hannes Floeckner;  peter 
(Sibbald at EMBL-Heidleberg.DE)

       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 E. Brenner    seb1005 at mbfs.bio.cam.ac.uk 

4.  MolViewer will read a 3d structure (connectivity information must also 

be present) and give you a list of backbone dihedrals which would be easy
to  
convert to 2ndary struct. However, it runs only under NeXTStep (ie, on a
NeXT  
or a 486 running NeXTStep). 

5. I don't know the software used to generate the information, but the
Brookhaven database entries contain helix, sheet, and turn assignments as
part of their ".ent" files.  The information is not strictly linear, as
helicies are grouped first, then all residues in sheets, then turns, but
residue numbers are provided in every case.  As a last resort, you could
even sort the data by hand, however it shouldn't take more than a small
program (even in BASIC if necessary) to sort out the information.  Note
that specialized structures are mentioned in the REMARKS section of the
.ent files.  Also, the Brookhaven Database is available on CDROM.
Stephen Aley                  saley at ucsd.edu



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