It can go both ways: If you increase atom radii by adding that of the
probe (e.g. 1.4 A° for a water probe) and calculate the "molecular
surface" using a zero probe with atom radii as previously defined (Ri
+1.4 A°), the area you get is that of the accessible surface.
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 19/01/2011 16:46, Richard Edward Gillilan wrote:
Since several people have asked me for code, I now realize that I've
contributed my bit to the confusion over names of various surface definitions.
To clear things up there is an excellent online article which covers the
history of various molecular surface definitions that I highly recommend:
www.netsci.org/Science/Compchem/feature14e.html
Mainly there are two related surface definitions:
(a) solvent-accessible surface
(b) molecular surface = contact surface + reentrant surface
"solvent-excluded volume" has been defined using both of the above. Both (a)
and (b) reduce to the same VDW surface when the solvent probe is zero.
There are also a number of smooth approximations to these definitions and
others.
Richard Gillilan
MacCHESS
