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