Publications

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Das, R., & Baker D. (2008).  Macromolecular modeling with rosetta. Annual review of biochemistry. 77, 363-82. Abstract  Download: das08A.pdf (1.13 MB)
Alm, E., & Baker D. (1999).  Matching theory and experiment in protein folding.. Current opinion in structural biology. 9(2), 189-96. Abstract
Grantcharova, V., Alm E. J., Baker D., & Horwich A. L. (2001).  Mechanisms of protein folding.. Current opinion in structural biology. 11(1), 70-82. Abstract
Baker, D. (1998).  Metastable states and folding free energy barriers.. Nature structural biology. 5(12), 1021-4.
Szeto, M. D., Boissel S. J. S., Baker D., & Thyme S. B. (2011).  Mining endonuclease cleavage determinants in genomic sequence data.. The Journal of biological chemistry. 286(37), 32617-27. Abstract
Dantas, G., Watters A. L., Lunde B. M., Eletr Z. M., Isern N. G., Roseman T., et al. (2006).  Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution. Journal of molecular biology. 362(5), 1004-24. Abstract  Download: dantas06A.pdf (1.15 MB)
Lacy, B. D., Lin H. C., Melnyk R. A., Schueler-Furman O., Reither L., Cunningham K., et al. (2005).  A model of anthrax toxin lethal factor bound to protective antigen. Proceedings of the National Academy of Sciences of the United States of America. 102(45), 16409-14. Abstract  Download: lacy05A.pdf (621.23 KB)
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)
Lee, M. R., Tsai J., Baker D., & Kollman P. A. (2001).  Molecular dynamics in the endgame of protein structure prediction. Journal of molecular biology. 313(2), 417-30. Abstract  Download: lee01B.pdf (814.49 KB)
Havranek, J. J., & Baker D. (2009).  Motif-directed flexible backbone design of functional interactions. Protein science. 18(6), 1293-305. Abstract  Download: havranek09A.pdf (753.33 KB)
Yarov-Yarovoy, V., Schonbrun J., & Baker D. (2006).  Multipass membrane protein structure prediction using Rosetta. Proteins. 62(4), 1010-25. Abstract  Download: yarov-yarovoy06B.pdf (1.31 MB)
Lengyel, C. S. E., Willis L. J., Mann P., Baker D., Kortemme T., Strong R. K., et al. (2007).  Mutations designed to destabilize the receptor-bound conformation increase MICA-NKG2D association rate and affinity. The Journal of biological chemistry. 282(42), 30658-66. Abstract  Download: lengyel07A.pdf (454.13 KB)