Andreas,
> ><plug>
> >You should probably have a look at the Macromolecular Structure
> >Database (msd.ebi.ac.uk) - it contains proposed biological assemblies,
> >calculated using an algorithm based on that used for PQS. You can
> >download PDB-format files from the website.
> ></plug>
> >
> >
> So in what respect do you think pdb files from MSD will be better than PQS?
> Since they both come from the EBI, they should be more or less the
> same,I assume - it would be schizofrenic to provide a good and bad
> version of quaternary structures...
> Well, I just discovered from your mail address, you would know!
I'm no expert in the details of either MSD or PQS, but I'd say the main
differences are
1. PQS files can contain the same problems that legacy PDB files do,
namely inconsistent naming of atoms and residues, possible duplication of
atom/residue numbers, incorrect stereochemistries etc. Compilation of the
MSD includes numerous checks for these things, in order to ensure that the
data is internally consistent, e.g. that all residues named 'XYZ' refer to
the same chemical compound.
2. The transformations used to generate biological assemblies in PQS
sometimes cause problems regarding ligands. PQS tries to assign a parent
chain to each ligand molecule, so that when protein chains are duplicated
and have symmetry operations applied to them, the ligand molecules get the
same treatment. For whatever reason, this sometimes does not work - I
have seen PQS files in which a ligand gets split in half, with some atoms
being transformed to a new symmetry mate, and some staying where they
are... This should not happen in the MSD due to the checks mentioned
above.
3. Apparently the algorithm used to generate MSD assemblies is not
*exactly* the same as that used in PQS, and I believe there is a greater
degree of manual curation applied to the results. So the structures you
get from MSD should agree with biological intutition more often (though
there is certainly no guarantee it will be 100% correct)
If you want to know more details, I'd suggest you contact the MSD team via
the address on their website.
Hope that helps,
Gareth
-------------------------------------------------------------------------------
Gareth Stockwell
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD gar...@ebi.ac.uk
Tel 01223 492548 http://www.ebi.ac.uk/~gareth
