Publications

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Malmström, L., Riffle M., Strauss C. E. M., Chivian D., Davis T. N., Bonneau R., et al. (2007).  Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS biology. 5(4), e76. Abstract  Download: malmström07A.pdf (592.42 KB)
McBeth, C., Seamons A., Pizarro J. C., Fleishman S. J., Baker D., Kortemme T., et al. (2008).  A new twist in TCR diversity revealed by a forbidden alphabeta TCR. Journal of molecular biology. 375(5), 1306-19. Abstract  Download: mcbeth08A.pdf (5.02 MB)
McCallister, E. L., Alm E., & Baker D. (2000).  Critical role of beta-hairpin formation in protein G folding. Nature structural biology. 7(8), 669-73. Abstract  Download: mccallister00A.pdf (785.9 KB)
McFarland, B. J., Kortemme T., Yu S. F., Baker D., & Strong R. K. (2003).  Symmetry recognizing asymmetry: analysis of the interactions between the C-type lectin-like immunoreceptor NKG2D and MHC class I-like ligands. Structure. 11(4), 411-22. Abstract  Download: mcfarland03A.pdf (2.83 MB)
Meiler, J., & Baker D. (2003).  Rapid protein fold determination using unassigned NMR data. Proceedings of the National Academy of Sciences of the United States of America. 100(26), 15404-9. Abstract  Download: meiler03B.pdf (593 KB)
Meiler, J., & Baker D. (2003).  Coupled prediction of protein secondary and tertiary structure. Proceedings of the National Academy of Sciences of the United States of America. 100(21), 12105-10. Abstract  Download: meiler03A.pdf (618.84 KB)
Meiler, J., & Baker D. (2006).  ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins. 65(3), 538-48. Abstract  Download: meiler06A.pdf (760.02 KB)
Meiler, J., & Baker D. (2005).  The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy. Journal of magnetic resonance. 173(2), 310-6. Abstract  Download: meiler05A.pdf (657.1 KB)
Millet, O., Mittermaier A., Baker D., & Kay L. E. (2003).  The effects of mutations on motions of side-chains in protein L studied by 2H NMR dynamics and scalar couplings. Journal of molecular biology. 329(3), 551-63. Abstract  Download: millet03A.pdf (1.03 MB)
Minard, P., Scalley-Kim M., Watters A., & Baker D. (2001).  A "loop entropy reduction" phage-display selection for folded amino acid sequences. Protein science. 10(1), 129-34. Abstract  Download: minard01A.pdf (229.21 KB)
Misura, K. M. S., & Baker D. (2005).  Progress and challenges in high-resolution refinement of protein structure models. Proteins. 59(1), 15-29. Abstract  Download: misura05A.pdf (651.28 KB)
Misura, K. M. S., Morozov A. V., & Baker D. (2004).  Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction. Journal of molecular biology. 342(2), 651-64. Abstract  Download: misura04A.pdf (867.48 KB)
Misura, K. M. S., Chivian D., Rohl C. A., Kim D. E., & Baker D. (2006).  Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proceedings of the National Academy of Sciences of the United States of America. 103(14), 5361-6. Abstract  Download: misura06A.pdf (2.12 MB)
Morozov, A. V., Havranek J. J., Baker D., & Siggia E. D. (2005).  Protein-DNA binding specificity predictions with structural models. Nucleic acids research. 33(18), 5781-98. Abstract  Download: morozov05A.pdf (293.94 KB)
Morozov, A. V., Tsemekhman K., & Baker D. (2006).  Electron density redistribution accounts for half the cooperativity of alpha helix formation. The journal of physical chemistry. B. 110(10), 4503-5. Abstract  Download: morozov06A.pdf (132.16 KB)
Morozov, A., Kortemme T., & Baker D. (2003).  Evaluation of Models of Electrostatic Interactions in Proteins. Journal of Physical Chemistry B. 107(9), 2075-2090. Abstract  Download: morozov03A.pdf (691.51 KB)
Morozov, A. V., Kortemme T., Tsemekhman K., & Baker D. (2004).  Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proceedings of the National Academy of Sciences of the United States of America. 101(18), 6946-51. Abstract  Download: morozov04A.pdf (444.99 KB)
Muratore, K. E., Seeliger M. A., Wang Z., Fomina D., Neiswinger J., Havranek J. J., et al. (2009).  Comparative analysis of mutant tyrosine kinase chemical rescue. Biochemistry. 48(15), 3378-86. Abstract  Download: muratore09A.pdf (318.66 KB)
Murphy, P. M., Bolduc J. M., Gallaher J. L., Stoddard B. L., & Baker D. (2009).  Alteration of enzyme specificity by computational loop remodeling and design. Proceedings of the National Academy of Sciences of the United States of America. 106(23), 9215-20. Abstract  Download: murphy09A.pdf (954.03 KB)