Member Site › Forums › Rosetta 3 › Rosetta 3 – General › how to transfer the rosetta score to physical unit?
- This topic has 7 replies, 4 voices, and was last updated 12 years, 2 months ago by
Anonymous.
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June 28, 2012 at 4:33 pm #1328
Anonymous
When predicting ddg, I find that the ddg has physical unit. But the score of design doesn’t. How to transfer the energy score to real physical unit? Thank you.
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June 28, 2012 at 6:19 pm #7350
attesor
I think the Rosetta Energy Score has no unit. Well, in their publications they use the unit named REU (Rosetta Energy Unit). I don’t think one can convert it to physical unit. But the scores are still comparable for the same protein, or protein of similar size.
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July 2, 2012 at 3:34 pm #7371
Anonymous
I do not suggest doing this, but because the scores are from a KBP, you should be able to use the reverse boltzmann equation to obtain the actual energy. See equation 1 of:
Knowledge Based Potentials: the Reverse Boltzmann
Methodology, Virtual Screening and Molecular Weight
DependenceChrysi Konstantinou Kirtay*a, John B. O. Mitchella and James A. Lumley
http://onlinelibrary.wiley.com/doi/10.1002/qsar.200430926/pdf -
June 28, 2012 at 8:23 pm #7352
Anonymous
In the ddG predicted program, it outputs kcal/mol as unit. I am not sure how the program get the real unit
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June 28, 2012 at 9:08 pm #7354
Anonymous
For the ddG application, there was a calibration set with experimentally known values that was compared to the ddG prediction in REUs, and from the line of best fit a conversion of prediction to kcal/mol was obtained. (See Kellogg et al. (2011) Proteins 79:830-838 for details)
Most of the other protocols have not be calibrated against experimental results. While people sometimes pull the calibration from one protocol to another, that’s not necessarily the most accurate thing to do. The absolute energies (and to a lesser extent the relative energies) you get are dependent on the protocol you use and how extensive the sampling is. And while there might be theoretical reasons to hope that there is a universal correlation between REU and kcal/mol for all situation, there hasn’t been the experimental validation done to confirm that.
So unless you have a test set which you can calibrate a particular protocol against, the general recommendation is to set aside the notion that you can directly convert from REU to kcal/mol, and instead just treat the output as a general “lower=better” metric. (Also keep in mind that even if you have a calibration curve, in all likelihood it will be incredibly noisy, netting you an order of magnitude estimation at best.)
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July 3, 2012 at 2:49 pm #7376
Anonymous
Thank you very much!
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July 3, 2012 at 9:20 pm #7378
Anonymous
Thanks!
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July 3, 2012 at 2:50 pm #7377
Anonymous
Thank you all~
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