Dear All,
I want to know, if it is correct to do molecular dynamics of only a single domain or part of the protein (like 5-6 A from the attached substrate)?
Is it acceptable in publications?
That depends on whether or not such a simulation addresses some kind of scientifically relevant question, or if it's just a shortcut to try to speed things up.
Thanks Justin for the answer.
Most of the time we go ahead and try to find a suitable way to cut of the time for simulation as running a program cost a load of money. So I just want to know if a ligand is attached to a motif of protein. is it OK to simulate only that part of the protein.
If not then why is it OK to remove one chain of a protein?
The answer depends on whether or not any longer-range dynamics are important. Often times they are. It's impossible to say without considering the biology of the problem.
Removing an entire chain also depends on context. If, for instance, a protein crystallizes as a dimer but is a functional monomer, it is not necessary or reasonable to simulate the dimer. If the functional unit is a dimer and the second chain is stripped away as a shortcut, I think that's wrong without very strong justification based on the biological function of the protein and known physics.
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