[gmx-users] on the dissociation of protein complex during MD

[Mark Abraham]

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.

Mark
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