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Macromolecular modeling and design in Rosetta: recent methods and frameworks.
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.
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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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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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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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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Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance.
Mavor D, Barlow KA, Asarnow D, Birman Y, Britain D, Chen W, Green EM, Kenner LR, Mensa B, Morinishi LS, Nelson CA, Poss EM, Suresh P, Tian R, Arhar T, Ary BE, Bauer DP, Bergman ID, Brunetti RM, Chio CM, Dai SA, Dickinson MS, Elledge SK, Helsell CVM, Hendel NL, Kang E, Kern N, Khoroshkin MS, Kirkemo LL, Lewis GR, Lou K, Marin WM, Maxwell AM, McTigue PF, Myers-Turnbull D, Nagy TL, Natale AM, Oltion K, Pourmal S, Reder GK, Rettko NJ, Rohweder PJ, Schwarz DMC, Tan SK, Thomas PV, Tibble RW, Town JP, Tsai MK, Ugur FS, Wassarman DR, Wolff AM, Wu TS, Bogdanoff D, Li J, Thorn KS, O'Conchúir S, Swaney DL, Chow ED, Madhani HD, Redding S, Bolon DN, Kortemme T, DeRisi JL, Kampmann M, Fraser JS.
Mavor D, et al. Among authors: o conchuir s.
Biol Open. 2018 Jul 23;7(7):bio036103. doi: 10.1242/bio.036103.
Biol Open. 2018.
PMID: 30037883
Free PMC article.
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