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
while evaluating it, you might want to check the importance of buried
residues by looking at how conserved they are in homologs.
tommi
Quoting Eleanor Dodson <[EMAIL PROTECTED]>:
> I dont know the answer but have you looked at the PISA site at the eBI -
>
> there is extensive documentation addr
Sebastiano,
I can suggests one approach to finding core residues..
CCP4mg will calculate the total asa buried per residue and residues can be
selected by the criteria of their buried area. One way to define the protein
core would be to select residues with, say, <5.0A*2 asa. You can easily se
I dont know the answer but have you looked at the PISA site at the eBI -
there is extensive documentation addressing these sorts of questions.
http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
Eleanor
Sebastiano Pasqualato wrote:
Hi all,
a few days ago I sent a post in which I was asking if an
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
