Publications

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Alexandrova, A. N., Röthlisberger D., Baker D., & Jorgensen W. L. (2008).  Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination. Journal of the American Chemical Society. 130(47), 15907-15. Abstract  Download: alexandrova08A.pdf (4.49 MB)
Alm, E., Morozov A. V., Kortemme T., & Baker D. (2002).  Simple physical models connect theory and experiment in protein folding kinetics. Journal of molecular biology. 322(2), 463-76. Abstract  Download: alm02A.pdf (1.2 MB)
Alm, E., & Baker D. (1999).  Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proceedings of the National Academy of Sciences of the United States of America. 96(20), 11305-10. Abstract  Download: alm99A.pdf (574.66 KB)
Alm, E., & Baker D. (1999).  Matching theory and experiment in protein folding.. Current opinion in structural biology. 9(2), 189-96. Abstract
Althoff, E. A., Wang L., Jiang L., Giger L., Lassila J. K., Wang Z., et al. (2012).  Robust design and optimization of retroaldol enzymes.. Protein science : a publication of the Protein Society. 21(5), 717-26. Abstract
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)
André, I., Bradley P., Wang C., & Baker D. (2007).  Prediction of the structure of symmetrical protein assemblies. Proceedings of the National Academy of Sciences of the United States of America. 104(45), 17656-61. Abstract  Download: André07A.pdf (1.15 MB)
Ashworth, J., Taylor G. K., Havranek J. J., Quadri A. S., Stoddard B. L., & Baker D. (2010).  Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs. Nucleic acids research. 38(16), 5601-8. Abstract  Download: ashworth10.pdf (3.02 MB)
Ashworth, J., Havranek J. J., Duarte C. M., Sussman D., Monnat R. J., Stoddard B. L., et al. (2006).  Computational redesign of endonuclease DNA binding and cleavage specificity. Nature. 441(7093), 656-9. Abstract  Download: ashworth06A.pdf (664.23 KB)
Ashworth, J., & Baker D. (2009).  Assessment of the optimization of affinity and specificity at protein-DNA interfaces. Nucleic acids research. 37(10), e73. Abstract  Download: ashworth09A.pdf (3.58 MB)
AV, M., KMS M., K T., & D B. (2004).  Comparison of Quantum Mechanics and Molecular Mechanics Dimerization Energy Landscapes for Pairs of Ring-Containing Amino Acids in Proteins. Journal of Physical Chemistry B . Abstract  Download: morozov04B.pdf (287.34 KB)
Azoitei, M. L., Ban Y. - E. A., Julien J. - P., Bryson S., Schroeter A., Kalyuzhniy O., et al. (2012).  Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope. Journal of molecular biology. 415(1), 175-92. Abstract  Download: azoitei12A.pdf (1.79 MB)
Azoitei, M. L., Correia B. E., Ban Y. - E. A., Carrico C., Kalyuzhniy O., Chen L., et al. (2011).  Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold. Science. 334(6054), 373-6. Abstract  Download: azoitei11A.pdf (2.01 MB)