Does any paper descript rosetta2.3's scoring function? I am confused by the scoring function in rosetta2.3 and rosetta3.3. Does them share the same energy terms and weights? Or where can I find out all these information? Thank you very much!
There are already many threads on these boards addressing (but not answering, there is no good answer), these questions. The best paper resources are the rohl methods in enzymology review and the supplemental to kuhlman's top7 paper in science.
2 and 3 share mostly the same terms and weights but there a lot of fine differences.
Thank you! But when I read the source code, I still can not figure out what terms are used in the rosetta2.3. In the score.cc score12()
barcode_weight = 1.0;
barcode_energy_weight = 0.00001;
taboo_weight = 1.0;
But these terms are not appear in the description of rosetta2.3.
I've never heard of those terms - I strongly suspect you can ignore them. Rosetta2.3 did a lot of funky stuff with if switches turning on bits of code only under certain conditions - those terms are probably not truly active.
Xavier tells me they (barcode at least) are used in fragment selection and fragment re-use (irrelevant for design). http://www.rosettacommons.org/guide/File+Format#_Barcode_constraints