Publications

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Ruohola-Baker, H., Grell E., Chou T. B., Baker D., Jan L. Y., & Jan Y. N. (1993).  Spatially localized rhomboid is required for establishment of the dorsal-ventral axis in Drosophila oogenesis. Cell. 73(5), 953-65. Abstract  Download: ruohola-baker93A.pdf (18.04 MB)
Ruohola, H., Bremer K. A., Baker D., Swedlow J. R., Jan L. Y., & Jan Y. N. (1991).  Role of neurogenic genes in establishment of follicle cell fate and oocyte polarity during oogenesis in Drosophila.. Cell. 66(3), 433-49. Abstract  Download: ruoholaa91.pdf (0 bytes)
Ruczinski, I., Kooperberg C., Bonneau R., & Baker D. (2002).  Distributions of beta sheets in proteins with application to structure prediction. Proteins. 48(1), 85-97. Abstract  Download: ruczinski02A.pdf (1017.65 KB)
Röthlisberger, D., Khersonsky O., Wollacott A. M., Jiang L., DeChancie J., Betker J., et al. (2008).  Kemp elimination catalysts by computational enzyme design. Nature. 453(7192), 190-5. Abstract  Download: röthlisberger08A.pdf (744.82 KB)
Rosato, A., Aramini J. M., Arrowsmith C., Bagaria A., Baker D., Cavalli A., et al. (2012).  Blind testing of routine, fully automated determination of protein structures from NMR data. Structure. 20(2), 227-36. Abstract
Rosato, A., Bagaria A., Baker D., Bardiaux B., Cavalli A., Doreleijers J. F., et al. (2009).  CASD-NMR: critical assessment of automated structure determination by NMR. Nature methods. 6(9), 625-6. Download: rosato09A.pdf (175.47 KB)
Rohl, C. A., Strauss C. E. M., Misura K. M. S., & Baker D. (2004).  Protein structure prediction using Rosetta.. Methods in enzymology. 383, 66-93.
Rohl, C. A., Strauss C. E. M., Chivian D., & Baker D. (2004).  Modeling structurally variable regions in homologous proteins with rosetta. Proteins. 55(3), 656-77. Abstract  Download: rohl04A.pdf (425.56 KB)
Rohl, C. A., & Baker D. (2002).  De novo determination of protein backbone structure from residual dipolar couplings using Rosetta. Journal of the American Chemical Society. 124(11), 2723-9. Abstract  Download: rohl02A.pdf (265.13 KB)
Riddle, D. S., Grantcharova V. P., Santiago J. V., Alm E., Ruczinski I., & Baker D. (1999).  Experiment and theory highlight role of native state topology in SH3 folding. Nature structural biology. 6(11), 1016-24. Abstract  Download: riddle99A.pdf (951.11 KB)
Riddle, D. S., Santiago J. V., Bray-Hall S. T., Doshi N., Grantcharova V. P., Yi Q., et al. (1997).  Functional rapidly folding proteins from simplified amino acid sequences. Nature structural biology. 4(10), 805-9. Abstract  Download: riddle97A.pdf (671.68 KB)
Richter, F., Blomberg R., Khare S. D., Kiss G., Kuzin A. P., Smith A. J. T., et al. (2012).  Computational design of catalytic dyads and oxyanion holes for ester hydrolysis.. Journal of the American Chemical Society. 134(39), 16197-206. Abstract
Rank, J. A., & Baker D. (1998).  Contributions of solvent-solvent hydrogen bonding and van der Waals interactions to the attraction between methane molecules in water. Biophysical chemistry. 71(2-3), 199-204. Abstract  Download: rank98A.pdf (120.64 KB)
Rank, J. A., & Baker D. (1997).  A desolvation barrier to hydrophobic cluster formation may contribute to the rate-limiting step in protein folding. Protein science. 6(2), 347-54. Abstract  Download: rank97A.pdf (1.76 MB)
Ramelot, T. A., Raman S., Kuzin A. P., Xiao R., Ma L. - C., Acton T. B., et al. (2009).  Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study. Proteins. 75(1), 147-67. Abstract  Download: ramelot09A.pdf (790.67 KB)
Raman, S., Vernon R., Thompson J., Tyka M., Sadreyev R., Pei J., et al. (2009).  Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins. 77 Suppl 9, 89-99. Abstract  Download: raman09A.pdf (500.47 KB)
Raman, S., Lange O. F., Rossi P., Tyka M., Wang X., Aramini J., et al. (2010).  NMR structure determination for larger proteins using backbone-only data. Science. 327(5968), 1014-8. Abstract  Download: raman10A.pdf (2.02 MB)
Raman, S., Huang Y. J., Mao B., Rossi P., Aramini J. M., Liu G., et al. (2010).  Accurate automated protein NMR structure determination using unassigned NOESY data. Journal of the American Chemical Society. 132(1), 202-7. Abstract  Download: raman10A.pdf (3.49 MB)