Going through the paper by Elizabeth Kellog et al in Proteins, i realized that the standard reference energies are not well optimized for Delta-deltaG calculation but more suited for sequence recovery. However, it is stated that a new set of opt-E weights yields better correlation. Can any one help me out in figuring where these new set of reference weights exists and how to incorporate them in the standard score12 function.
Thanks in advance
I can seem to find any mention of what those weights actually are, either in the paper or in the codebase.
To actually apply them, you would make a copy of the appropriate weights file (e.g. rosetta_database/scoring/weights/score12_full.wts), and then modify the "METHOD_WEIGHTS ref" line. The numbers following are the reference energies for each amino acid type (in alphabetical one letter code order, i.e. A C D E ...)