Start here:
Methods Enzymol. 2004;383:66-93.
Protein structure prediction using Rosetta.
Rohl CA, Strauss CE, Misura KM, Baker D.
PMID: 15063647 [PubMed]
http://www.ncbi.nlm.nih.gov/pubmed/15063647
and here:
Science. 2003 Nov 21;302(5649):1364-8.
Design of a novel globular protein fold with atomic-level accuracy.
Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D.
http://www.ncbi.nlm.nih.gov/pubmed/14631033
This describes most of the scorefunction terms as of 7 years ago. Their base forms haven’t changed much although they’ve been tweaked.
I don’t think we’ve published a review of the scorefunction since 3.0, but if I forgot one someone please correct me. There’s a major review of the overhauls in the 3.x series that’s been submitted but it doesn’t talk about the scorefunction forms, since they didn’t change much.
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