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

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