wrote:
I'm wondering if using DOPE assessment is only possible to evaluate each chains indvidually. Once I get the DOPE score of the two chains, how to combine them to get an unique DOPE score for my complex? Is summing the two (or more) score reasonable? Other way, what If I create my complex as a single chain?
You seem to be going to a lot of trouble to work around a non-existent limitation. See also http://salilab.org/archives/modeller_usage/2007/msg00329.html
The issue is that multi-chain models were not included in the DOPE benchmark set. You can try to work around this in any of the ways you describe, but that doesn't change the fact that your models are multi-chain. I suggest you just score your whole complex as is.
You could certainly score each chain separately and combine the scores, but then you'd be missing out on the inter-chain interactions, so I don't see what you would buy you.
Ben Webb, Modeller Caretaker
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