Michel Cuendet wrote:
Hi list,
I wanted to post something about g_sas some time ago already, but didn't
find time to. Here is the occasion.
I believe g_sas does not actually compute the solvent accessible surface
area (SASA, defined as the locus of the center of the probe sphere), but
rather the molecular surface (defined using the surface of the probe
sphere). See
http://www.netsci.org/Science/Compchem/feature14e.html
This should really be explained in the help of g_sas, together with the
references for the algorithm used. It would also be nice to have an
option to calculate the true SASA, in addition to the molecular surface.
The reference to the algorithm is also printed when you run the program.
The algorithm used gives basically the same result as the MSMS program
from Scripps.
How is the DGsolv calculated by g_sas? and the areas ? which algorithm?
where is the code? reference?
The code would be in g_sas.c, would be my guess.
The reference is in the code.
"D. Eisenberg and A. D. McLachlan",
"Solvation energy in protein folding and binding",
"Nature",
319, 1986, "199-203"
This method is completely different from the way nonpolar solvation free
energy is calculated in implicit solvation models such as GBSA, which is
based on the true SASA. The method of Eisenberg seems more detailed
though, because it attributes different weights to surface patches
depending on the type of the underlying atom. It would be interesting to
know why this method has not been more widely used.
This free energy estimate is close to useless, but easy to compute.
When using Amber atom types it would also be possible to use a slightly
more modern variant (JPCB 105 (2001) 5055), which is not necessarily a
lot better though.
Best,
Michel
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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