- This topic has 4 replies, 5 voices, and was last updated 8 years, 8 months ago by Anonymous.
October 21, 2009 at 2:48 am #351Anonymous
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?
October 21, 2009 at 1:49 pm #4245Anonymous
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.
March 23, 2015 at 10:21 pm #10887Anonymous
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
March 25, 2015 at 5:53 pm #10891
March 30, 2015 at 9:43 pm #10911Anonymous
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.)
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