> In my research project I need to do simulation on a protein with a lot
> of intramolecular hydrogen bonds (more the better). Does anyone know
> about a protein with maximum number of intramolecular hydrogen bonds in
> it; or is there any way by which I can get such a structure from PDB?
This is what I would do:
.. Download all the PDBs of proteins.
.. Write a script that:
-> 'Protonates' (say using tleap/protonate) the protein atoms
-> Finds all intra-molecular h-bonds (defining group SOLUTE in carnal)
-> Count the number of such h-bonds.
>From the table of PDB-ID vs number of h-bonds, I'll pickup the protien of
interest.
The toughest part here is to d/l the PDBs, the rest is quite simple. And
also you need to know what is the kind of 'protein' you wish to (and can)
simulate (like single chain/multiple and total number of atoms). I
wouldn't attempt to pickup a viral-coat protein, a proteosome, a ribosome
or some structure with 5 angstrom resolution! So somewhere, probably
before the h-bond calculation, I'd check the size of the system to see if
I need to consider it at all!
Best wishes,
-Sanjeev
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Received on Sat Nov 27 2004 - 15:53:00 PST
