moldpdf, DOPE score and GA341 score
Dear users,
I am a new user of Modeller. I have the following results:
>> Summary of successfully produced models: Filename molpdf DOPE score GA341 score ---------------------------------------------------------------------- qseq1.B99990001.pdb 8602.63281 -113144.73438 1.00000 qseq1.B99990002.pdb 8773.10840 -113346.03125 1.00000 qseq1.B99990003.pdb 8349.71387 -112852.75000 1.00000 qseq1.B99990004.pdb 9365.16406 -111568.75781 1.00000 qseq1.B99990005.pdb 8553.98926 -112664.98438 1.00000
1.) What is "moldpdf", "DOPE score" and "GA341 score"? What is the meaning of them? 2.) how will I determine the best result according to the above table/results? What is the best result?
Thanks in advance
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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Ahmet yıldırım -
Modeller Caretaker