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
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