[gmx-users] on the dissociation of protein complex during MD
Mark.Abraham at anu.edu.au
Thu Mar 1 02:46:56 CET 2012
On 1/03/2012 11:57 AM, Dialing Pretty wrote:
> Dear All,
> Some of the complexes of PDB files in RCSB are not from
> protein-protein interaction, but from the packing of protein crystal.
> Thus in solution the "protien complex" may dissociate.
> However as for the protein are usually very large, and I regard it is
> difficult to observe that 2 (or more) subunit protein complex
> dissociate completely during MD simulation.
> Can you please introduce to me your experience that the "protein
> complex" sifnificantly dissociate during MD?
That's a very expensive way to observe whether the complex is thought to
be "real" or not - if it is possible to get a reliable result. Reading
the literature that led to the PDB contribution and about the protein
generally will be much more productive.
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