Subject: CCL: Re: calculate accessible surface area for an occluded cavity

From: Michel Petitjean <ptitjean-.at.-itodys.jussieu.fr>
Date: Thu, 8 Apr 2004 11:01:38 +0200 (MEST)

To: <chemistry-.at.-ccl.net>
Subj: CCL: Re: calculate accessible surface area for an occluded cavity

Dear Qin,

May I suggest two ways. I assume that you know which residues are
on the boundary on the cavity. Using adequate radii, the SAS can
be computed either analytically, or by Monte-Carlo (faster, but less
accurate), with the freeware ASV: binaries and documentation with
reference in:
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ASV
Also, if you have a roughly convex cavity (e.g. the convex hull of
the alpha-carbons bounding the cavity), you can get the surface
of the hull (and its generalized radius and diameter), with the
free ware RADI: binaries and documentation with reference in:
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#RADI
 
Michel Petitjean,                     Email: petitjean-.at.-itodys.jussieu.fr
ITODYS (CNRS, UMR 7086)                      ptitjean-.at.-ccr.jussieu.fr
1 rue Guy de la Brosse                Phone: +33 (0)1 44 27 48 57
75005 Paris, France.                  FAX  : +33 (0)1 44 27 68 14
http://petitjeanmichel.free.fr/itoweb.petitjean.html
..................................................................
> From owner-chemistry-.at.-ccl.net Thu Apr  8 08:19:56 2004
From: "Q" <qzou-.at.-iupui.edu>
To: <chemistry-.at.-ccl.net>
Subject: CCL:calculate accessible surface area for an occluded cavity
Date: Wed, 7 Apr 2004 19:29:58 -0500

Dear All,
 I have a protein with an internal cavity that has no access to the =
outside solvent. I would like to calculate the accessible surface area =
of the residues inside the cavity to see how accessible they are to the =
cavity. How can I do this or what programs could help to do it? How =
about NACCESS? Thanks for any input.

Qin