VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 29 2002 - 09:49:31 CST

Hi Vlad,
  VMD uses the program Stride to calculate secondary structure.
The reference for Stride is printed in VMD when you use the "cartoon"
rep, or the sequence viewer:

Info) In any publication of scientific results based in part or
Info) completely on the use of the program STRIDE, please reference:
Info) Frishman,D & Argos,P. (1995) Knowledge-based secondary structure
Info) assignment. Proteins: structure, function and genetics, 23, 566-579.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Oct 29, 2002 at 11:34:57AM +0100, Vlad Cojocaru wrote:
> Could somebody tell me how the secondary structure of a protein is
> calculated in vMD or give a reference?
> Thanks a lot,
> vlad
>
> --
> Vlad Cojocaru
> Max Planck Institut for Biophysical Chemistry
> Deparment: 060
> Am Fassberg 11, 37077 Goettingen, Germany
> tel: ++49-551-201.1389
> e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078