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Page 1
Scaffolding protein functional sites using deep learning.
Wang J, Lisanza S, Juergens D, Tischer D, Watson JL, Castro KM, Ragotte R, Saragovi A, Milles LF, Baek M, Anishchenko I, Yang W, Hicks DR, Expòsit M, Schlichthaerle T, Chun JH, Dauparas J, Bennett N, Wicky BIM, Muenks A, DiMaio F, Correia B, Ovchinnikov S, Baker D. Wang J, et al. Among authors: correia b. Science. 2022 Jul 22;377(6604):387-394. doi: 10.1126/science.abn2100. Epub 2022 Jul 21. Science. 2022. PMID: 35862514 Free PMC article.
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. Among authors: correia be. 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.
De novo protein design enables the precise induction of RSV-neutralizing antibodies.
Sesterhenn F, Yang C, Bonet J, Cramer JT, Wen X, Wang Y, Chiang CI, Abriata LA, Kucharska I, Castoro G, Vollers SS, Galloux M, Dheilly E, Rosset S, Corthésy P, Georgeon S, Villard M, Richard CA, Descamps D, Delgado T, Oricchio E, Rameix-Welti MA, Más V, Ervin S, Eléouët JF, Riffault S, Bates JT, Julien JP, Li Y, Jardetzky T, Krey T, Correia BE. Sesterhenn F, et al. Science. 2020 May 15;368(6492):eaay5051. doi: 10.1126/science.aay5051. Science. 2020. PMID: 32409444 Free PMC article.
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: correia be. 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.
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. 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
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. 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.
215 results