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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: ford as. 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.
Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites.
Hosseinzadeh P, Watson PR, Craven TW, Li X, Rettie S, Pardo-Avila F, Bera AK, Mulligan VK, Lu P, Ford AS, Weitzner BD, Stewart LJ, Moyer AP, Di Piazza M, Whalen JG, Greisen PJ, Christianson DW, Baker D. Hosseinzadeh P, et al. Among authors: ford as. Nat Commun. 2021 Jun 7;12(1):3384. doi: 10.1038/s41467-021-23609-8. Nat Commun. 2021. PMID: 34099674 Free PMC article.
De novo protein design by citizen scientists.
Koepnick B, Flatten J, Husain T, Ford A, Silva DA, Bick MJ, Bauer A, Liu G, Ishida Y, Boykov A, Estep RD, Kleinfelter S, Nørgård-Solano T, Wei L, Players F, Montelione GT, DiMaio F, Popović Z, Khatib F, Cooper S, Baker D. Koepnick B, et al. Nature. 2019 Jun;570(7761):390-394. doi: 10.1038/s41586-019-1274-4. Epub 2019 Jun 5. Nature. 2019. PMID: 31168091 Free PMC article.
Computational design of a synthetic PD-1 agonist.
Bryan CM, Rocklin GJ, Bick MJ, Ford A, Majri-Morrison S, Kroll AV, Miller CJ, Carter L, Goreshnik I, Kang A, DiMaio F, Tarbell KV, Baker D. Bryan CM, et al. Proc Natl Acad Sci U S A. 2021 Jul 20;118(29):e2102164118. doi: 10.1073/pnas.2102164118. Proc Natl Acad Sci U S A. 2021. PMID: 34272285 Free PMC article.
Large-scale design and refinement of stable proteins using sequence-only models.
Singer JM, Novotney S, Strickland D, Haddox HK, Leiby N, Rocklin GJ, Chow CM, Roy A, Bera AK, Motta FC, Cao L, Strauch EM, Chidyausiku TM, Ford A, Ho E, Zaitzeff A, Mackenzie CO, Eramian H, DiMaio F, Grigoryan G, Vaughn M, Stewart LJ, Baker D, Klavins E. Singer JM, et al. PLoS One. 2022 Mar 14;17(3):e0265020. doi: 10.1371/journal.pone.0265020. eCollection 2022. PLoS One. 2022. PMID: 35286324 Free PMC article.
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