structure calculation

Andras Szilagyi szia at enzim.hu
Wed May 17 06:51:27 EST 1995

In article <Pine.SOL.3.91.950516164851.9538B-100000-100000-100000 at topaz>, 
chan at bioch.ox.ac.uk says...
>Hi there,
>Can anyone tell me is there a software that can calculate the phi and 
>angles of each amino acid residue from pdb files. The reason is that I 
>want to know which strach of amino acid is alpha-coil, beta-sheet, turn 
>and random coil _calculated_ from the pdb files. That means, not 
>prediction. I have try to extract the molscript file from rasmol, but 
>result is not very good.
>Thanks in advance!
>*         2     *       Christopher Chan                             *
>*   CCCCC       *       Dept. of Biochemistry                        *
>*   C           *       University of Oxford                         *
>*   C           *       Oxford                                       *
>*   C           *       U.K.                                         *
>*   CCCCC       *       Tel.: 0865-(2)75239                          *
>*               *       E-mail: chan at bioch.ox.ac.uk                  *
>----- PGP public key available upon request -----

The program that you need is DSSP by Kabsch and Sander. It is free for 
academic use, however, you should sign and send to the authors a license 
agreement. The program takes a PDB file and calculates the secondary 
structure based on the main chain hydrogen bonding pattern (this is more 
reliable and precise than definitions based on dihedral angles). It 
defines helices, sheets, turns, 3-10 helices, Pi-helices, bends, and 
isolated beta bridges. The output file also contains accessibilities for 
each residue and the phi and psi angles. This program has become a 
standard of secondary structure definition. The reference is:
Kabsch,W. and Sander,C. (1983) Biopolymers 22:2577-2637.

The contact person is Chris Sander:
   Current address for Chris Sander:
   Biocomputing, EMBL, 6900 Heidelberg, Germany
   Telephone: +49-6221-387 361 Telex: 461613 embl d
   Telefax:   +49-6221-387 306
E-mail: sander at embl-heidelberg.de

Hope this helps,
Andras Szilagyi (szia at enzim.hu)
Institute of Enzymology, Hungarian Academy of Sciences

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