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    Rosetta’s energy function has evolved over the years, and unfortunately there is no one publication I can point you to that will explain how each of the scorefunction terms works and how they relate to one another. Start with the recent reviews and track backwards is the best advice I can give. Rohl et al., 2004 (Methods in Enzymology) along with the supplementary info for the Top7 paper (Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D (2003-11-21). “Design of a novel globular protein fold with atomic-level accuracy”. Science 302 (5649): 1364–1368. doi:10.1126/science.1089427. PMID 14631033.) are good places to start.