Noah's Publications in our lab
- 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. 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.
- Koehler Leman J, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J; RosettaCommons Consortium, Bystroff C, Schief W, Gront D, Schueler-Furman O, Baker D, Bradley P, Dunbrack R, Kortemme T, Leaver-Fay A, Strauss CEM, Meiler J, Kuhlman B, Gray JJ, Bonneau R. Better together: Elements of successful scientific software development in a distributed collaborative community. PLoS Comput Biol. 2020 May 4;16(5):e1007507. doi: 10.1371/journal.pcbi.1007507.
- Glasgow AA*, Huang YM*, Mandell DJ*, Thompson M, Ritterson R, Loshbaugh AL, Pellegrino J, Krivacic C, Pache RA, Barlow KA, Ollikainen N, Jeon D, Kelly MJS, Fraser JS, Kortemme T. Computational design of a modular protein sense-response system. Science. 2019 Nov 22;366(6468):1024-1028. doi: 10.1126/science.aax8780. *co-first author
- Ollikainen, N, de Jong, RM, Kortemme, T. Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity. PLoS Comput Biol. 2015 Sep 23;11(9):e1004335. doi: 10.1371/journal.pcbi.1004335
- Ó Conchúir, S, Barlow, KA, Pache, RA, Ollikainen, N, Kundert, K, O'Meara, MJ, Smith, CA, Kortemme, T. A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design. PLoS One. 2015 Sep 3;10(9):e0130433. doi:10.1371/journal.pone.0130433
- Melero, C*, Ollikainen, N*, Harwood, I, Karpiak, J, Kortemme, T. Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition. Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15426-31. doi: 10.1073/pnas.1410624111. *co-first author
- Jackson, EL, Ollikainen, N, Covert, AW 3rd, Kortemme, T, Wilke, CO. Amino-acid site variability among natural and designed proteins. PeerJ. 2013 Nov 12;1:e211. doi: 10.7717/peerj.211
- Ollikainen, N, Kortemme, T. Computational Protein Design Quantifies Structural Constraints on Amino Acid Covariation. PLoS Comput Biol 9(11):e1003313, 2013. doi: 10.1371/journal.pcbi.1003313
- Ollikainen, N, Smith, CA, Fraser, JS, Kortemme, T. Chapter Four - Flexible Backbone Sampling Methods to Model and Design Protein Alternative Conformations in Methods in Enzymology Volume 523 (Methods in Protein Design):61-85, 2013. doi: 10.1016/B978-0-12-394292-0.00004-7
- Ollikainen, N, Sentovich, E, Coelho, C, Kuehlmann, A, Kortemme, T. SAT-based protein design. Proceedings of the 2009 IEEE/ACM International Conference on Computer-Aided Design (ICCAD 2009) (Computer-Aided Design - Digest of Technical Papers, 2009. ICCAD 2009. IEEE/ACM International Conference on):128-35, 2009.