[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [modeller_usage] Question about DOPE



Wei Chen wrote:
I read something about DOPE. I understand it is a statistical potential. I followed tutorials to calculate the DOPE profile. Someone said that DOPE profile is calculted by Potential Energy / Restriction. In the tutorial, it seems that DOPE profile should be above - 0.03. My question is why it shoud be above -0.03. Why is the potential energy positive if it is above -0.03?

The profile, just like the DOPE score itself, is just an energy measure (the profile shown in the tutorial is energy/number of restraints, for each residue). Thus, it is not normalized, and any cutoff you choose is arbitrary.

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage