VMD-L Mailing List

From: Timothy Driscoll (molvisions_at_mac.com)
Date: Wed Oct 26 2005 - 17:52:39 CDT

On Oct 26, 2005, at 2:13 p, John Stone wrote:

>
> Hi,
> There's some information on STRIDE here, with references
> to the relevant papers that describe the algorithms it uses:
> http://wolf.bi.umist.ac.uk/unix/stride.html
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Oct 26, 2005 at 01:57:08PM -0400, Stanley Lan wrote:
>
>> Just out of curiosity, does the program locate the area of the fy
>> and sy
>> angle on the Ramachandran plot to determine whether if it's alpha
>> or beta
>> configuration?
>>
>> -Stanley

IIRC, Stride uses dihedral calculations and hydrogen bond contacts,
but not homology, to assign secondary structure.

tim 

-- 
Timothy Driscoll
molvisions - see. grasp. learn.
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