Wanted: program to extract secondary struct from pdb files

matte at skyfox.usask.ca matte at skyfox.usask.ca
Tue May 17 14:47:13 EST 1994


> Description: Wanted: program to extract secondary struct from pdb files

> I am looking for a program that will take the atomic coordinates of PDB
> files and calculate the secondary structure, based on phi and psi angles
> of the residues. I have several PDB files that are missing the secondary
> structure information, and I need this info for several of my programs. My
> mentor told me that there was one such program developed by Kabsch and
> Sander (EMBL, Heidelberg). Where can I find it, or any other program?

> Thanks in advance.

> Steven Adams, Graduate Student, Biochemistry, Baylor College of Medicine
> email: sa690538 at bcm.tmc.edu


	There is a program developed at the Centre for Structural Biology,
Yale University, called DEFINE_Structure which will do secondary structures
based on c-alpha coordinates. See F.M. Richards and C.E. Kundrot Proteins
3:71-84 (1988) Identification of Structural Motifs from Protein Coordinate Data:
Secondary Structure and First-Level  Supersecondary Structure. You will need
to contact the authors and get permission to download the program from Yale;
I believe there is no cost. 

Hope this helps !

-------------------------------------------------------------------------------
| Allan Matte                          |                                      |
| Department of Biochemistry           | Phone: (306)966-4366                 |
| University of Saskatchewan           | Fax: (306)966-8718                   |
| Saskatoon, Saskatchewan              | E-mail: matte at sask.usask.ca          |
| CANADA S7N 0W0                       |                                      |
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