Shane's Publications in our lab

  1. Krivacic C*, Kundert K*, Pan X*, Pache RA*, Liu L, Conchúir SO, Jeliazkov JR, Gray JJ, Thompson MC, Fraser JS, & Kortemme T.  Accurate positioning of functional residues with robotics-inspired computational protein design. Proc Natl Acad Sci U S A, 2022;119(11), e2115480119. https://doi.org/10.1073/pnas.2115480119 *co-first author
  2. ​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.
  3. 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. ​
  4. 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. Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance. Biol Open. pii: bio036103. 2018. doi: 10.1242/bio.036103. ​
  5. Barlow KA, Ó Conchúir S, Thompson S, Suresh P, Lucas JE, Heinonen M, Kortemme T. Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein-Protein Binding Affinity upon Mutation. J Phys Chem B. 2018 doi: 10.1021/acs.jpcb.7b11367. 
  6. Mavor, D, Barlow, KA, Thompson, S, Barad, BA, Bonny, AR, Cario, CL, Gaskins, G, Liu, Z, Deming, L, Axen, SD, Caceres, E, Chen, W, Cuesta, A, Gate, R, Green, EM, Hulce, KR, Ji, W, Kenner, LR, Mensa, B, Morinishi, LS, Moss, SM, Mravic, M, Muir, RK, Niekamp, S, Nnadi, CI, Palovcak, E, Poss, EM, Ross, TD, Salcedo, E, See, S, Subramaniam, M, Wong, AW, Li, J, Thorn, KS, Ó Conchúir, S, Roscoe, BP, Chow, ED, DeRisi, JL, Kortemme, T, Bolon, DN, Fraser, JS. Determination of Ubiquitin Fitness Landscapes Under Different Chemical Stresses in a Classroom Setting. Elife. pii: e15802.  2016. doi: 10.7554/eLife.15802
  7. 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 *co-first author
  8. Lyskov, S, Chou, F, Ó Conchúir, S, Der, BS, Drew, K, Kuroda, D, Xu, J, Weitzner, BD, Renfrew, PD, Sripakdeevong, P, Borgo, B, Havranek, JJ, Kuhlman, B, Kortemme, T, Bonneau, R, Gray, JJ, Das, R. Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE). PLoS ONE 8(5):e63906, 2013. doi: 10.1371/journal.pone.0063906
  9. Humphris-Narayanan, EL, Akiva, E, Varela, R, Ó Conchúir, S, Kortemme, T. Prediction of Mutational Tolerance in HIV-1 Protease and Reverse Transcriptase Using Flexible Backbone Protein Design. PLoS Comput Biol 8(8):e1002639, 2012. doi: 10.1371/journal.pcbi.1002639​