[gmx-users] antiparallel beta sheet

[Justin Lemkul]

On 3/3/14, 2:02 PM, Nidhi Katyal wrote:
> Dear users,
>
> I would like to analyse the time variation of antiparallel beta sheet
> formation. I am aware that dssp and stride program can calculate the beta
> sheet content but is there a tool that can distinguish between antiparallel
> and parallel beta sheet (in terms of giving numeric value as output and not
> through visual inspection)?
>

You can define an order parameter between 0 and 1 to discriminate between the 
two.  It is fairly common in simulation literature of amyloids.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================