Rosetta is the result of years of academic research, across dozens of labs. If you use Rosetta in your research, we ask that you follow academic good citizenship and cite it appropriately.
The Rosetta package as a whole is a combination of multiple different sub-protocols, each described in their own papers. There is no one single reference which is "The Rosetta Citation". Instead, the appropriate reference(s) to cite are the ones which describe the particular protocol you are using. As protocols are made of different substeps, there may be multiple papers which are necessary to cite to appropriately reference Rosetta.
As an aide to locating appropriate papers, Rosetta sometimes prints out citation information for protocols used during the run at the end. This list of citations is not exhaustive. Many protocols and references (particularly older ones) are missing from that list. Some references which are listed as "unpublished" have since been published, but the Rosetta output has not been updated. Additionally, a reference being printed simply means that a section of the code related to that paper has been called. It does not mean that reference is the most appropriate reference for the protocol as-a-whole which you are using. Please read and understand the papers listed and incorporate them into your citations appropriately.
Often times the best way of finding the reference for the protocol you used is to examine where you first learned about the protocol (e.g. another paper or documentation page) and look for citation information that way.
The following list of papers is not intended to be exhaustive, but merely an attempt to provide starting points to search for other related papers.
Please also see the "Rosetta canon" page of the documentation for a list of seminal papers for various different modeling approaches.
Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, Ban YE, Fleishman SJ, Corn JE, Kim DE, Lyskov S, Berrondo M, Mentzer S, Popović Z, Havranek JJ, Karanicolas J, Das R, Meiler J, Kortemme T, Gray JJ, Kuhlman B, Baker D, Bradley P. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol. 2011;487:545-74. doi: 10.1016/B978-0-12-381270-4.00019-6.
Fleishman SJ, Leaver-Fay A, Corn JE, Strauch EM, Khare SD, Koga N, Ashworth J, Murphy P, Richter F, Lemmon G, Meiler J, Baker D. RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite. PLoS One. 2011;6(6):e20161. doi: 10.1371/journal.pone.0020161.
Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL Jr, Das R, Baker D, Kuhlman B, Kortemme T, Gray JJ. The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design. J Chem Theory Comput. 2017 Jun 13;13(6):3031-3048. doi: 10.1021/acs.jctc.7b00125. Epub 2017 May 12. Erratum in: J Chem Theory Comput. 2022 Jul 12;18(7):4594.
Leman JK, et. al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nat Methods. 2020 Jul;17(7):665-680. doi: 10.1038/s41592-020-0848-2