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Page 1
Macromolecular modeling and design in Rosetta: recent methods and frameworks.
Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, Bradley P, Bystroff C, Conway P, Cooper S, Correia BE, Coventry B, Das R, De Jong RM, DiMaio F, Dsilva L, Dunbrack R, Ford AS, Frenz B, Fu DY, Geniesse C, Goldschmidt L, Gowthaman R, Gray JJ, Gront D, Guffy S, Horowitz S, Huang PS, Huber T, Jacobs TM, Jeliazkov JR, Johnson DK, Kappel K, Karanicolas J, Khakzad H, Khar KR, Khare SD, Khatib F, Khramushin A, King IC, Kleffner R, Koepnick B, Kortemme T, Kuenze G, Kuhlman B, Kuroda D, Labonte JW, Lai JK, Lapidoth G, Leaver-Fay A, Lindert S, Linsky T, London N, Lubin JH, Lyskov S, Maguire J, Malmström L, Marcos E, Marcu O, Marze NA, Meiler J, Moretti R, Mulligan VK, Nerli S, Norn C, Ó'Conchúir S, Ollikainen N, Ovchinnikov S, Pacella MS, Pan X, Park H, Pavlovicz RE, Pethe M, Pierce BG, Pilla KB, Raveh B, Renfrew PD, Burman SSR, Rubenstein A, Sauer MF, Scheck A, Schief W, Schueler-Furman O, Sedan Y, Sevy AM, Sgourakis NG, Shi L, Siegel JB, Silva DA, Smith S, Song Y, Stein A, Szegedy M, Teets FD, Thyme SB, Wang RY, Watkins A, Zimmerman L, Bonneau R. Leman JK, et al. Among authors: bonet j. Nat Methods. 2020 Jul;17(7):665-680. doi: 10.1038/s41592-020-0848-2. Epub 2020 Jun 1. Nat Methods. 2020. PMID: 32483333 Free PMC article. Review.
Rosetta FunFolDes - A general framework for the computational design of functional proteins.
Bonet J, Wehrle S, Schriever K, Yang C, Billet A, Sesterhenn F, Scheck A, Sverrisson F, Veselkova B, Vollers S, Lourman R, Villard M, Rosset S, Krey T, Correia BE. Bonet J, et al. PLoS Comput Biol. 2018 Nov 19;14(11):e1006623. doi: 10.1371/journal.pcbi.1006623. eCollection 2018 Nov. PLoS Comput Biol. 2018. PMID: 30452434 Free PMC article.
A computationally designed chimeric antigen receptor provides a small-molecule safety switch for T-cell therapy.
Giordano-Attianese G, Gainza P, Gray-Gaillard E, Cribioli E, Shui S, Kim S, Kwak MJ, Vollers S, Corria Osorio AJ, Reichenbach P, Bonet J, Oh BH, Irving M, Coukos G, Correia BE. Giordano-Attianese G, et al. Among authors: bonet j. Nat Biotechnol. 2020 Apr;38(4):426-432. doi: 10.1038/s41587-019-0403-9. Epub 2020 Feb 3. Nat Biotechnol. 2020. PMID: 32015549
Author Correction: A computationally designed chimeric antigen receptor provides a small-molecule safety switch for T-cell therapy.
Giordano-Attianese G, Gainza P, Gray-Gaillard E, Cribioli E, Shui S, Kim S, Kwak MJ, Vollers S, Corria Osorio AJ, Reichenbach P, Bonet J, Oh BH, Irving M, Coukos G, Correia BE. Giordano-Attianese G, et al. Among authors: bonet j. Nat Biotechnol. 2020 Apr;38(4):503. doi: 10.1038/s41587-020-0461-z. Nat Biotechnol. 2020. PMID: 32127717
Bottom-up de novo design of functional proteins with complex structural features.
Yang C, Sesterhenn F, Bonet J, van Aalen EA, Scheller L, Abriata LA, Cramer JT, Wen X, Rosset S, Georgeon S, Jardetzky T, Krey T, Fussenegger M, Merkx M, Correia BE. Yang C, et al. Among authors: bonet j. Nat Chem Biol. 2021 Apr;17(4):492-500. doi: 10.1038/s41589-020-00699-x. Epub 2021 Jan 4. Nat Chem Biol. 2021. PMID: 33398169
Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design.
Schoeder CT, Schmitz S, Adolf-Bryfogle J, Sevy AM, Finn JA, Sauer MF, Bozhanova NG, Mueller BK, Sangha AK, Bonet J, Sheehan JH, Kuenze G, Marlow B, Smith ST, Woods H, Bender BJ, Martina CE, Del Alamo D, Kodali P, Gulsevin A, Schief WR, Correia BE, Crowe JE Jr, Meiler J, Moretti R. Schoeder CT, et al. Among authors: bonet j. Biochemistry. 2021 Mar 23;60(11):825-846. doi: 10.1021/acs.biochem.0c00912. Epub 2021 Mar 11. Biochemistry. 2021. PMID: 33705117 Free PMC article.
RosettaSurf-A surface-centric computational design approach.
Scheck A, Rosset S, Defferrard M, Loukas A, Bonet J, Vandergheynst P, Correia BE. Scheck A, et al. Among authors: bonet j. PLoS Comput Biol. 2022 Mar 16;18(3):e1009178. doi: 10.1371/journal.pcbi.1009178. eCollection 2022 Mar. PLoS Comput Biol. 2022. PMID: 35294435 Free PMC article.
A generic framework for hierarchical de novo protein design.
Harteveld Z, Bonet J, Rosset S, Yang C, Sesterhenn F, Correia BE. Harteveld Z, et al. Among authors: bonet j. Proc Natl Acad Sci U S A. 2022 Oct 25;119(43):e2206111119. doi: 10.1073/pnas.2206111119. Epub 2022 Oct 17. Proc Natl Acad Sci U S A. 2022. PMID: 36252041 Free PMC article.
261 results