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 see what has been selected in the molecular graphics and try varying the criteria if necessary. If you need to do this for many structures we could write a script. Liz On Tuesday 19 June 2007 09:55, 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
