Please cite the following article when referring to results from our ROSIE server:
- PatchMAN: A. Khramushin, Z. Ben-Aharon, T. Tsaban, J.K. Varga, O. Avraham, O. Schueler-Furman, Matching protein surface structural patches for high-resolution blind peptide docking, *Proc. Natl. Acad. Sci. U.S.A.* 119:e2121153119, https://doi.org/10.1073/pnas.2121153119 (2022).
- MASTER: J. Zhou, G. Grigoryan, Rapid Search for Tertiary Fragments Reveals Protein Sequence-Structure Relationships, *Protein Science* 24:508-524 https://doi.org/10.1002/pro.2610 (2015).
- Canner SW, Schnaar RL, Gray JG., "The Proteome as a Lectome: Predictions from Deep Learning Propose Substantial Protein-Carbohydrate Interplay" [full citation pending]
- Ref2015 – Alford et al. 10.1038/s41592-020-0848-2.
- Genpot - Park et al. 10.1021/acs.jctc.0c01184.
- Ligand - Smith & Meiler 10.1371/journal.pone.0240450.
- Raveh B, London N, Schueler-Furman O. (2010). Sub-angstrom modeling of complexes between flexible peptides and globular proteins. Proteins 78:2029-40. [PMID: 20455260]
- London N, Raveh B, Cohen E, Fathi G, Schueler-Furman O. (2011). Rosetta FlexPepDock web server - high resolution modeling of peptide-protein interactions. Nucleic Acids Research 2011. [PMID: 21622962]
- Harmalkar A, Lyskov S, Gray JJ, “Reliable protein-protein docking with AlphaFold, Rosetta and replica-exchange.” bioRxiv, 2023. https://doi.org/10.1101/2023.07.28.551063 [online]
- Thieker, D. F., Maguire, J. B., Kudlacek, S. T., Leaver‐Fay, A., Lyskov, S., & Kuhlman, B. (2022). Stabilizing proteins, simplified: A Rosetta‐based webtool for predicting favorable mutations. Protein Science, 31(10), e4428. [online]
- Marze NA, Roy Burman SS, Sheffler W & Gray JJ "Efficient Flexible Backbone Protein-Protein Docking for Challenging Targets," Bioinformatics 34(20):3461-3469 (2018) [online]
- Turzo, S.B.A.; Seffernick, J.T.; Rolland, A.D.; Donor, M.T.; Heinze, S.; Prell, J.S.; Wysocki, V.H.; Lindert, S. (2022), "Protein shape sampled by ion mobility mass spectrometry consistently improves protein structure prediction" Nat Commun 13 (1), 4377 Online.
- Jeliazkov JR, Frick R, Zhou J, Gray JJ "Robustification of RosettaAntibody and Rosetta SnugDock," PLoS ONE 16(3):e0234282 (2021) Online.
- Lyskov S, Chou FC, Conchúir SÓ, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, Gray JJ, Das R., "Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)" PLoS One. 2013 May 22;8(5):e63906. doi: 10.1371/journal.pone.0063906. Print 2013. [online]
Citations for individual score functions, please reference one that appropriate:
Modeling tools developed by FurmanLab@HUJI. The ROSIE implementation was developed by Sergey Lyskov and Julia Varga.