Publications

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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)
Wedemeyer, W. J., & Baker D. (2003).  Efficient minimization of angle-dependent potentials for polypeptides in internal coordinates. Proteins. 53(2), 262-72. Abstract  Download: wedemeyer03A.pdf (363.38 KB)
Tyka, M. D., Jung K., & Baker D. (2012).  Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers.. Journal of computational chemistry. 33(31), 2483-91. Abstract
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)
Ofek, G., Guenaga J. F., Schief W. R., Skinner J., Baker D., Wyatt R., et al. (2010).  Elicitation of structure-specific antibodies by epitope scaffolds. Proceedings of the National Academy of Sciences of the United States of America. 107(42), 17880-7. Abstract  Download: ofek10A.pdf (2.68 MB)
André, I., Strauss C. E. M., Kaplan D. B., Bradley P., & Baker D. (2008).  Emergence of symmetry in homooligomeric biological assemblies. Proceedings of the National Academy of Sciences of the United States of America. 105(42), 16148-52. Abstract  Download: andré08A.pdf (588.8 KB)
Wargacki, A. J., Leonard E., Win M. N., Regitsky D. D., Santos C. N. S., Kim P. B., et al. (2012).  An engineered microbial platform for direct biofuel production from brown macroalgae. Science. 335(6066), 308-13. Abstract  Download: wargacki12A.pdf (1.41 MB)
Baker, D., & DeGrado W. F. (1999).  Engineering and design. Current opinion in structural biology. 9(4), 485-6.
Baxter, S., Lambert A. R., Kuhar R., Jarjour J., Kulshina N., Parmeggiani F., et al. (2012).  Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases.. Nucleic acids research. 40(16), 7985-8000. Abstract
Kellogg, E. H., Lange O. F., & Baker D. (2012).  Evaluation and optimization of discrete state models of protein folding.. The journal of physical chemistry. B. 116(37), 11405-13. Abstract
Kiss, G., Röthlisberger D., Baker D., & Houk K. N. (2010).  Evaluation and ranking of enzyme designs. Protein science. 19(9), 1760-73. Abstract  Download: kiss10A.pdf (884.51 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)
Saunders, C. T., & Baker D. (2002).  Evaluation of structural and evolutionary contributions to deleterious mutation prediction. Journal of molecular biology. 322(4), 891-901. Abstract  Download: saunders02A.pdf (484.42 KB)
Plaxco, K. W., Larson S., Ruczinski I., Riddle D. S., Thayer E. C., Buchwitz B., et al. (2000).  Evolutionary conservation in protein folding kinetics. Journal of molecular biology. 298(2), 303-12. Abstract  Download: plaxco00a.pdf (214.04 KB)
Baker, D. (2010).  An exciting but challenging road ahead for computational enzyme design. Protein science.  Download: baker10A.pdf (58.56 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)
Keeble, A. H., Joachimiak L. A., Maté M. J., Meenan N., Kirkpatrick N., Baker D., et al. (2008).  Experimental and computational analyses of the energetic basis for dual recognition of immunity proteins by colicin endonucleases. Journal of molecular biology. 379(4), 745-59. Abstract  Download: keeble08A.pdf (1.25 MB)
Thyme, S. B., Jarjour J., Takeuchi R., Havranek J. J., Ashworth J., Scharenberg A. M., et al. (2009).  Exploitation of binding energy for catalysis and design. Nature. 461(7268), 1300-4. Abstract  Download: thyme09A.pdf (971.19 KB)