[Owl-devel] Pisa connection

[Dan Bolser]

On 31 May 2010 18:07, Jose M. Duarte <jose.m.duarte at gmail.com> wrote:
> Hi Henning
>
> Ok so I'll try to reply all of them:
>
> On 31 May 2010 15:52, Henning Stehr <stehr at molgen.mpg.de> wrote:
>>
>> Hi Jose,
>>
>> the stuff in owl.connections.pisa looks amazing. Just some quick
>> questions. What I'm interested in is getting the residues which are
>> involved in protein-protein interfaces in the most likely assembly.
>>
>
> Right now I've only implemented the parsing of interfaces description and
> not that of assemblies. It shouldn't be too difficult to parse the XML
> assembly description files though.
>
>
>>
>> 1. Are the interfaces returned by getInterfacesDescription()
>> automatically taken from the "best" assembly or all assemblies or some
>> other default one?
>
> Those are all possible interfaces found by the PISA algorithm
>
>
>>
>> 2. I assume that PisaInterface.firstMolecule and
>> PisaInterface.secondMolecule are the two molecules which are in
>> contact via the interface. If the assembly is e.g. a homo-dimer, would
>> firstMolecule and secondMolecule then be the same?
>
> Not necessarily. The thing is the PisaMolecule objects contain the whole
> description of the interface including all the BSAs of residues involved.
> Even in the case of a homo-dimer, the interfaces on both sides can be
> different.
>
>
>>
>> 3. Say I list the residues by PisaInterface.getFirst().getResidues().
>> Are these only the ones in contact in this interface (and this
>> assembly) or all residues in the chain/molecule?
>
> They are all residues in the interface. To get the subset of contacting
> residues you will have to filter by using the BSA values
> (PisaResidue.getBsa()). Basically the getRimAndCore() method is doing that
> but returning a PisaRimCore object which divides the contacting residues in
> core ones (above the BSA cut-off) and rim (BSA>0 but below the cut-off).
>
>
>> 4. Currently you are downloading pre-calculated data for existing PDB
>> codes, right? How different/difficult would it be to get data for
>> custom uploaded structures?
>
> Right now all I'm doing is accessing the pre-calculated PISA data available
> for download in XML format (see
> http://www.ebi.ac.uk/msd-srv/prot_int/pi_download.html). Doing it for custom
> structures would be quite difficult. It would require parsing the html,
> dealing with cookies, well you know the whole pain of reverse-engineering
> the site...
>
>
>>
>> 5. Maybe a question for the other Pisa experts on the list: Would it
>> even make sense to run such delicate calculations as Pisa does on
>> predicted structures?
>
> I would say it doesn't make sense. Pisa needs pretty accurate interface
> descriptions in order to work properly. But that's just a gut feeling, don't
> quote me on that ;-)

Are you predicting PPIs?

If so, awesome! If not, PISA isn't an appropriate tool, because (I'm
assuming) you aren't dealing with symmetry.

Pisa uses information on h-bonds, for example, so if your interface is
refined enough to include structures like that, it should work. It
would be interesting to find out... how many docked proteins 'fall
apart' in PISA.



>
>
>>
>> BTW, did you know there is also a standalone version of PISA in CCP4?
>> (see http://smb.slac.stanford.edu/facilities/software/ccp4/html/pisa.html)
>
> Yes, I tried that one also but then I realise it was very out of date and
> doesn't seem to be getting updated anymore. I don't remember exactly but
> there were something like 6 releases between that and the live one on the
> PISA web site (with many important features added in between).
>
> Hope it helps
>
> Jose
>
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