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Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance.
Biol Open. 2018 Jul 23;7(7):bio036103. doi: 10.1242/bio.036103.
Biol Open. 2018.
PMID: 30037883
Free PMC article.
Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein-Protein Binding Affinity upon Mutation.
Barlow KA, Ó Conchúir S, Thompson S, Suresh P, Lucas JE, Heinonen M, Kortemme T.
Barlow KA, et al. Among authors: o conchuir s.
J Phys Chem B. 2018 May 31;122(21):5389-5399. doi: 10.1021/acs.jpcb.7b11367. Epub 2018 Feb 15.
J Phys Chem B. 2018.
PMID: 29401388
Free PMC article.
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A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design.
Ó Conchúir S, Barlow KA, Pache RA, Ollikainen N, Kundert K, O'Meara MJ, Smith CA, Kortemme T.
Ó Conchúir S, et al.
PLoS One. 2015 Sep 3;10(9):e0130433. doi: 10.1371/journal.pone.0130433. eCollection 2015.
PLoS One. 2015.
PMID: 26335248
Free PMC article.
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Prediction of mutational tolerance in HIV-1 protease and reverse transcriptase using flexible backbone protein design.
Humphris-Narayanan E, Akiva E, Varela R, Ó Conchúir S, Kortemme T.
Humphris-Narayanan E, et al. Among authors: o conchuir s.
PLoS Comput Biol. 2012;8(8):e1002639. doi: 10.1371/journal.pcbi.1002639. Epub 2012 Aug 23.
PLoS Comput Biol. 2012.
PMID: 22927804
Free PMC article.
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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: o conchuir s.
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.
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Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks.
Koehler Leman J, Lyskov S, Lewis SM, Adolf-Bryfogle J, Alford RF, Barlow K, Ben-Aharon Z, Farrell D, Fell J, Hansen WA, Harmalkar A, Jeliazkov J, Kuenze G, Krys JD, Ljubetič A, Loshbaugh AL, Maguire J, Moretti R, Mulligan VK, Nance ML, Nguyen PT, Ó Conchúir S, Roy Burman SS, Samanta R, Smith ST, Teets F, Tiemann JKS, Watkins A, Woods H, Yachnin BJ, Bahl CD, Bailey-Kellogg C, Baker D, Das R, DiMaio F, Khare SD, Kortemme T, Labonte JW, Lindorff-Larsen K, Meiler J, Schief W, Schueler-Furman O, Siegel JB, Stein A, Yarov-Yarovoy V, Kuhlman B, Leaver-Fay A, Gront D, Gray JJ, Bonneau R.
Koehler Leman J, et al. Among authors: o conchuir s.
Nat Commun. 2021 Nov 29;12(1):6947. doi: 10.1038/s41467-021-27222-7.
Nat Commun. 2021.
PMID: 34845212
Free PMC article.
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