Hello -- I'm trying to understand the all-atom energy functions that Rosetta is using, and the best documentation that I have available is:
Protein Structure Prediction Using Rosetta
By Carol A. Rohl, Charlie E. M. Strauss, Kira M. S. Misura, and David Baker
Methods Enzymol. 2004;383:66-93.
Is there any documentation available that is more up-to-date with the source code?
That's the reference we use too. The core energy function formulae haven't really changed since then, we improve Rosetta by adding new score terms and reweighting instead. If a new important term comes out it usually gets its own paper (for example, the hydrogen bonding term.)
There are some papers in the works on the transition to 3.x and on the reweighting code but neither have been submitted.
Any chance I could get an author-copy of "Protein Structure Prediction Using Rosetta"? I'm at a UW lab (I have a UW email, all verifiable). Unfortunately, it looks like our school journal access doesn't include access to the publication http://www.sciencedirect.com/science/article/pii/S0076687904830040
Most of the Baker Lab publications can actually be downloaded from the Baker Lab website ( http://www.bakerlab.org/biblio/ ). (David is part of HHMI, which requires free dissemination of publications.)
Unfortunately, that particular publication is not available from the website. I would recommend doing an "article request" from your institutions inter-library loan site. (See, for example http://www.lib.washington.edu/ill ) Most university libraries have such a program, and the article requests are usually free for people at the university. (The thought is that they save money by not getting a subscription to a rarely-read journal, and only paying per-article costs for the rare cases when someone needs a particular article.)