I have a few question concerning the energy terms computed by MODELLER: 1) Can the energy of a model computed with loop-modeling be compared to the energy of a model computed without? 2) Can the energy of a model with an additional constraint added (like a specific distance constraint) be compared to the energy of a model without that specific constraint? 3) What kind of energy difference can be considered to reflect a significant difference in the quality of models?
Sincerely, Dan Thomas Major
-- Dan Thomas Major (at Dr. B. Fischer's lab) Bar-Ilan University
Phone: 972-3-5317785 Fax: 972-3-5348730
HEllo,
1. No. 2. No. 3. depends on the magnitude of the score, but tipically the lowest few scores do not represent meaningfully different models.
reason for 1 and 2 is that modeller scores solely depend on the violation of restrainst, adding or removing some of them will setup a new relative pseudo-energy scale.
best wishes, Andras
Dan Thomas Major wrote: > > I have a few question concerning the energy terms computed by > MODELLER: > 1) Can the energy of a model computed with loop-modeling be compared > to the energy of a model computed without? > 2) Can the energy of a model with an additional constraint added (like > a specific distance constraint) be compared to the energy of a model > without that specific constraint? > 3) What kind of energy difference can be considered to reflect a > significant difference in the quality of models? > > Sincerely, > Dan Thomas Major > > -- > Dan Thomas Major (at Dr. B. Fischer's lab) > Bar-Ilan University > > Phone: 972-3-5317785 > Fax: 972-3-5348730 > >
participants (2)
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Andras Fiser -
Dan Thomas Major