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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