Where can I find information that explains what the score values are and how to interpret and compare them? I’m new to Rosetta and still trying to learn what is going on while I learn how to run the program; so excuse me if I missed something obvious. Also, is the primary source of information related to Rosetta in published papers or is there something more explanatory than the Rosetta manual? Thanks for any help.
The Rohl 2004 review paper has some of the seeds of the energy function; the Kuhlman 2003 (Top7) paper has the other half. The recent Leaver-Fay review has the structure of the ScoreFunction but not really its science.
Most of the details are in those two papers, with the rest scattered elsewhere. There’s not a secret trove of information (short of the developers’ collective memories).