Dear Tea,
I'm still not quie sure what exactly would you like to do.
Nevertheless, there are a few things that could probably help
you.
You can certainly try acccesible surface area (ASA) calculations
as was already suggested....there are many ASA calculating
programs available, I should probably mention AREAIMOL as this is
ccp4bb....AREAIMOL is a part of the ccp4 package....
You can also try to compare how conserved the surfaces are in
terms of sequence with ConSurf:
http://consurf.tau.ac.il
You might also want to have a look at the recent work from the
Janet Thornton's group...see these papers:
Real
spherical harmonic expansion coefficients as 3D shape descriptors for
protein binding pocket and ligand comparisons
PMID:
15728116
A method for
localizing ligand binding pockets in protein structures.
PMID:
16304646
- a work that combines both above mentioned methods
And if you want to work with already deposited structures, you
can look at their electrostatic surfaces here:
http://ef-site.hgc.jp/eF-site/
good luck,
--
--marian
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Marian
Novotny
Department of Cell & Molecular Biology
Uppsala University
BMC Box 596
Uppsala
SE-75124
Sweden
Department of Cell & Molecular Biology
Uppsala University
BMC Box 596
Uppsala
SE-75124
Sweden
Phone:
+46-18-471-4872
mailto:[EMAIL PROTECTED]
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