Hi,
There exists a formal analytical way in doing this using the "survol"
command in BRUGEL package.
In short, this command define the accessible surface (external and
cavities) to the probe you choose and creates
separate masks (ensembles) of all atoms/residues that define these surfaces.
The way to go, then, would be to create a collection mask of all
accessible atoms/residues and subtract this
from your protein mask to be left with the mask that contains the core
residues.
You could also use a cutoff of 5-10% ASA max (there are different ways
of calculating these !).
On the other hand, taking away even residues that display very little
ASA (< 5%) would certainly leave you with
genuine core residues.
Hope this helps.
Greetings,
Pr. Nadir T. Mrabet
Cellular & Molecular Biochemistry
INSERM U-724
UHP - Nancy 1, School of Medicine
Avenue de la Foret de Haye, BP 184
54505 Vandoeuvre-les-Nancy Cedex
France
Phone: +33 (0)3.83.68.32.73
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Sebastiano Pasqualato wrote:
Hi all,
a few days ago I sent a post in which I was asking if anybody knew a
program to automatically define the hydrophobic core of a protein,
given the pdb.
Unfortunately I got no answers, and indeed a more thorough googling
around revealed that such a program might not exist.
So it seems I have to define my hydrophobic core residues by hand...
So now my question would be: how to define the hydrophobic core residues?
I would tend to say that those that bury more than ## % (say 70%, 80%
??) of their otherwise solvent accessible surface area could be
defined as such, but how can I get such a /per residue/ percentage?
(NB: this is not the asa buried upon interaction, so I don't know how
to get the asa of the "free" amino acid)
Alternatively, are there other simple and defined rules to state which
are the hydrophobic core residues?
Any help appreciated,
thanks in advance,
ciao
s
--
Sebastiano Pasqualato, PhD
IFOM-IEO Campus
Dipartimento di Oncologia Sperimentale
Istituto Europeo di Oncologia
via Adamello, 16
20139 Milano
Italy
tel +39 02 9437 5094
fax +39 02 574 303 310
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