Good points Richard!
The ambiguity with surface definition starts with the assumption that
atoms are (i) spheres and (ii) with fixed radii.
I am not sure Connolly was able to sell his original algorithm due to
conflicts of interest with the Scripps, where it had been actually
developped first.
How could I get the Varshney code?
Best regards,
Nadir
Pr. Nadir T. Mrabet
Structural& Molecular Biochemistry
Nutrigenex - INSERM U-954
Nancy University, School of Medicine
9, Avenue de la Foret de Haye, BP 184
54505 Vandoeuvre-les-Nancy Cedex
France
Phone: +33 (0)3.83.68.32.73
Fax: +33 (0)3.83.68.32.79
E-mail: Nadir.Mrabet<at> medecine.uhp-nancy.fr
Cell.: +33 (0)6.11.35.69.09
On 13/01/2011 13:40, Richard Edward Gillilan wrote:
:
*Subject: **Re: [ccp4bb] What is the simplest method to analytically
compute the Solvent-Accessible Surface Area of a given atom in a protein?*
My knowledge on this is probably quite out of date by now, but some
years ago there was a lot of research on this topic because such
surfaces are important in electrostatics and implicit solvation models
(calculating surface area) as well as molecular graphics.
I think the most widely-used definition of a solvent-accessible
surface is Lee-Richards surface in which a solvent-sized sphere is
rolled along the surface of the protein. Surface is therefore
rigorously defined as a piecewise collection of convex and concave
patches of spheres and tori. It was Connolly who implemented (and
sold) a practical algorithm for computing these surfaces. They were
even known as Connolly surfaces and rendered as dots before modern
computing hardware allowed for rendering surfaces. Several groups have
developed high-efficiency versions of the calculation. Harold
Scheraga's group, for example, has some FORTRAN code for this. Fred
Brook's virtual reality group also developed a high-effeciency
parallel version (Varshney was the guy's name I think) in C. There
have been many approximations over the years I think ... but you asked
about analytical models.
The these algorithms are non trivial. That's a understatement. And
there is actually a mathematical ambiguity in the surface definition
itself.
The Varshney code is freely available ... I received email permission
from both Varshney and his thesis advisor to freely distribute the
code. I even offered it to Warren Delano years ago when he was writing
Pymol, but he refused to include it because he felt there still might
be legal issues that would effect Pymol. So ... Pymol contains only a
somewhat improvised an non-rigorous surface algorithm (last time I
looked). Fine for graphics of course.
en.wikipedia.org/wiki/Accessible_surface_area
<http://en.wikipedia.org/wiki/Accessible_surface_area>
Richard
On Jan 13, 2011, at 1:00 AM, Francois Berenger wrote:
Hello,
Does someone know some good articles on this particular topic?
I'd like to implement the thing myself, however if there is
a good software doing the job (with readable source code),
I might use and cite it.
Best regards,
Francois.
