VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Aug 10 2012 - 06:42:54 CDT

On Fri, Aug 10, 2012 at 11:46 AM, Jeremy Lucid <jerlucid_at_gmail.com> wrote:
> Which algorithm is used to calculate the Solvent Accessible surface area (
> SASA ) in VMD.
> A reference to the paper would be much appreciated.

i don't know if there is any publication, but the
basic algorithm is pretty straightforward to see
from the source code.

each atom is represented by 500 points randomly
spread on its surface and thus respresent 1/500th
of the surface area of that atom as determined by
its radius. then all neighboring atoms are checked.
if any of the 500 points are within the radius of these
atoms the points and their corresponding surface
area are removed from the total surface area.

HTH,
    axel.

> Jer 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.