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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