Publications

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Sawaya, M. R., Wojtowicz W. M., Andre I., Qian B., Wu W., Baker D., et al. (2008).  A double S shape provides the structural basis for the extraordinary binding specificity of Dscam isoforms. Cell. 134(6), 1007-18. Abstract  Download: sawaya08A.pdf (6.42 MB)
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)
Shcherbata, H. R., Yatsenko A. S., Patterson L., Sood V. D., Nudel U., Yaffe D., et al. (2007).  Dissecting muscle and neuronal disorders in a Drosophila model of muscular dystrophy. The EMBO journal. 26(2), 481-93. Abstract  Download: shcherbata07A.pdf (916.91 KB)
Yi, Q., & Baker D. (1996).  Direct evidence for a two-state protein unfolding transition from hydrogen-deuterium exchange, mass spectrometry, and NMR. Protein science. 5(6), 1060-6. Abstract  Download: yi96A.pdf (4.65 MB)
Sgourakis, N. G., Lange O. F., DiMaio F., André I., Fitzkee N. C., Rossi P., et al. (2011).  Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings. Journal of the American Chemical Society. Abstract  Download: sgourakis11A.pdf (655.81 KB)
Lange, O. F., Rossi P., Sgourakis N. G., Song Y., Lee H. - W., Aramini J. M., et al. (2012).  Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples.. Proceedings of the National Academy of Sciences of the United States of America. 109(27), 10873-8. Abstract
Thayer, E. C., Bystroff C., & Baker D. (2000).  Detection of protein coding sequences using a mixture model for local protein amino acid sequence. Journal of computational biology : a journal of computational molecular cell biology. 7(1-2), 317-27. Abstract  Download: thayer00A.pdf (244.63 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)
Chevalier, B. S., Kortemme T., Chadsey M. S., Baker D., Monnat R. J., & Stoddard B. L. (2002).  Design, activity, and structure of a highly specific artificial endonuclease. Molecular cell. 10(4), 895-905. Abstract  Download: chevalier02A.pdf (671.2 KB)
Kuhlman, B., Dantas G., Ireton G. C., Varani G., Stoddard B. L., & Baker D. (2003).  Design of a novel globular protein fold with atomic-level accuracy. Science. 302(5649), 1364-8. Abstract  Download: kuhlman03A.pdf (2.79 MB)
Shen, Y., Vernon R., Baker D., & Bax A. (2009).  De novo protein structure generation from incomplete chemical shift assignments. Journal of biomolecular NMR. 43(2), 63-78. Abstract  Download: shen09A.pdf (2.53 MB)
Bowers, P. M., Strauss C. E., & Baker D. (2000).  De novo protein structure determination using sparse NMR data.. Journal of biomolecular NMR. 18(4), 311-8. Abstract
Karanicolas, J., Corn J. E., Chen I., Joachimiak L. A., Dym O., Peck S. H., et al. (2011).  A De Novo Protein Binding Pair By Computational Design and Directed Evolution. Molecular cell. Abstract  Download: karanicolas11A.pdf (1.2 MB)
Bonneau, R., Strauss C. E. M., Rohl C. A., Chivian D., Bradley P., Malmström L., et al. (2002).  De novo prediction of three-dimensional structures for major protein families. Journal of molecular biology. 322(1), 65-78. Abstract  Download: bonneau02B.pdf (855.42 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)
Jiang, L., Althoff E. A., Clemente F. R., Doyle L., Röthlisberger D., Zanghellini A., et al. (2008).  De novo computational design of retro-aldol enzymes. Science. 319(5868), 1387-91. Abstract  Download: jiang08A.pdf (629.34 KB)