Re: [modeller_usage] Global DOPE vs. local profile

[Modeller Caretaker <modeller-care@ucsf.edu>]

hori koshii wrote:
> My other question is: what if the profile score for each of the residues 
> get lower (after MD simulation) but the global score actually increases?
>
> How could we compare the two models then? Would you say one is better 
> than the other because of (global DOPE or profile)?

You could perhaps argue that the structure of that part of the protein 
with a lowered DOPE score has improved, at the expense of some other 
part of the protein. But DOPE was designed and benchmarked primarily to 
score proteins, not individual residues, so I'd say the more reliable 
indicator is the global DOPE score.

	Ben Webb, Modeller Caretaker
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