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

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
--
             http://www.salilab.org/modeller/
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