Could anyone tell me where to find documentation for Talaris scoring function? I can’t find any description about it though it is the default energy function now. I try to understand why this scoring function is better than others’. Thank you!
There is some information in main/database/scoring/weights/talaris2013.wts
Basically, Talaris is a combination of a bunch of the assorted scorefunction fixes which had been percolating for a while. I don’t think there’s any one location where the details have been collected and benchmarking published, but several references are:
Leaver-Fay A et al. Methods Enzymol. 2013;523:109-43
Song Y et al. Proteins. 2011;79(6):1898-909.
Shapovalov, M.S., et al. Structure, 2011 19, 844-858.
Other parts of the Talaris2013 scorefunction have not yet been published. (But this is not too much different than the previous score12 scorefunction, where bits and pieces were published, but nothing describing the scorefunction as a whole was made. [Aside from various papers using the scorefunction as a whole.]) There’s some talk about publishing a Rosetta scorefunction review/description paper, but nothing has made it to the publication stage yet.
This paper describes the modifications to the score function — in particular to the hydrogen bonding potential — that came with the Talaris2013 and Talaris2014 weight sets. (It was published quite a bit after Rocco’s first post).