Re: [modeller_usage] moldpdf, DOPE score and GA341 score

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

On 1/23/13 5:00 AM, Ahmet yıldırım wrote:
> 1.) What is "moldpdf", "DOPE score" and "GA341 score"? What is the
> meaning of them?

molpdf is the Modeller objective function: 
http://salilab.org/modeller/9.11/manual/node468.html (or see the 
Modeller publication)
GA341: http://salilab.org/modeller/9.11/manual/node197.html
DOPE: http://salilab.org/modeller/9.11/manual/node253.html

> 2.) how will I determine the best result according to the above
> table/results? What is the best result?

"Best" depends on what you want to do with the model, but of those three 
scores, DOPE is the most reliable at separating native-like models from 
decoys (lower, i.e, more negative, DOPE scores tend to correlate with 
more native-like models).

	Ben Webb, Modeller Caretaker
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