Publications

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Kuhn, M., Meiler J., & Baker D. (2004).  Strand-loop-strand motifs: prediction of hairpins and diverging turns in proteins. Proteins. 54(2), 282-8. Abstract  Download: kuhn04A.pdf (219.88 KB)
Kuhlman, B., O'Neill J. W., Kim D. E., Zhang K. Y. J., & Baker D. (2002).  Accurate computer-based design of a new backbone conformation in the second turn of protein L. Journal of molecular biology. 315(3), 471-7. Abstract  Download: kuhlman02A.pdf (281.28 KB)
Kuhlman, B., O'Neill J. W., Kim D. E., Zhang K. Y., & Baker D. (2001).  Conversion of monomeric protein L to an obligate dimer by computational protein design. Proceedings of the National Academy of Sciences of the United States of America. 98(19), 10687-91. Abstract  Download: kuhlman01A.pdf (558.98 KB)
Kuhlman, B., & Baker D. (2000).  Native protein sequences are close to optimal for their structures. Proceedings of the National Academy of Sciences of the United States of America. 97(19), 10383-8. Abstract  Download: kuhlman00A.pdf (142.94 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)
Krieger, E., Joo K., Lee J., Lee J., Raman S., Thompson J., et al. (2009).  Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins. 77 Suppl 9, 114-22. Abstract  Download: krieger09A.pdf (646.49 KB)
Krantz, B. A., Srivastava A. K., Nauli S., Baker D., Sauer R. T., & Sosnick T. R. (2002).  Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects. Nature structural biology. 9(6), 458-63. Abstract  Download: krantz02A.pdf (2.41 MB)
Kortemme, T., & Baker D. (2004).  Computational design of protein-protein interactions. Current opinion in chemical biology. 8(1), 91-7. Abstract  Download: kortemme04A.pdf (204.71 KB)
Kortemme, T., Morozov A. V., & Baker D. (2003).  An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. Journal of molecular biology. 326(4), 1239-59. Abstract  Download: kortemmea03A.pdf (2.13 MB)
Kortemme, T., Kim D. E., & Baker D. (2004).  Computational alanine scanning of protein-protein interfaces. Science's STKE. 2004(219), pl2. Abstract  Download: kortemme04B.pdf (2.47 MB)
Kortemme, T., & Baker D. (2002).  A simple physical model for binding energy hot spots in protein-protein complexes. Proceedings of the National Academy of Sciences of the United States of America. 99(22), 14116-21. Abstract  Download: kortemme02A.pdf (200.71 KB)
Kortemme, T., Joachimiak L. A., Bullock A. N., Schuler A. D., Stoddard B. L., & Baker D. (2004).  Computational redesign of protein-protein interaction specificity. Nature structural & molecular biology. 11(4), 371-9. Abstract  Download: kortemme04A.pdf (1.2 MB)
Korkegian, A., Black M. E., Baker D., & Stoddard B. L. (2005).  Computational thermostabilization of an enzyme. Science. 308(5723), 857-60. Abstract  Download: korkegian05A.pdf (274.59 KB)
Koga, N., Tatsumi-Koga R., Liu G., Xiao R., Acton T. B., Montelione G. T., et al. (2012).  Principles for designing ideal protein structures.. Nature. 491(7423), 222-7. Abstract  Download: nature11600.pdf (2.17 MB)
Knight, J. D. R., Qian B., Baker D., & Kothary R. (2007).  Conservation, variability and the modeling of active protein kinases. PloS one. 2(10), e982. Abstract  Download: knight07A.pdf (2.64 MB)
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)
King, N. P., Sheffler W., Sawaya M. R., Vollmar B. S., Sumida J. P., André I., et al. (2012).  Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science. Abstract  Download: king12A.pdf (1.36 MB)
Kim, D. E., Blum B., Bradley P., & Baker D. (2009).  Sampling bottlenecks in de novo protein structure prediction. Journal of molecular biology. 393(1), 249-60. Abstract  Download: kim09A.pdf (1.12 MB)
Kim, D. E., Fisher C., & Baker D. (2000).  A breakdown of symmetry in the folding transition state of protein L. Journal of molecular biology. 298(5), 971-84. Abstract  Download: kim00A.pdf (416.01 KB)
Kim, D. E., Chivian D., & Baker D. (2004).  Protein structure prediction and analysis using the Robetta server. Nucleic acids research. 32(Web Server issue), W526-31. Abstract  Download: kim04A.pdf (890.15 KB)
Kim, D. E., Chivian D., Malmström L., & Baker D. (2005).  Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM. Proteins. 61 Suppl 7, 193-200. Abstract  Download: kim05A.pdf (683.21 KB)
Kim, K. M., Yi E. C., Baker D., & Zhang K. Y. (2001).  Post-translational modification of the N-terminal His tag interferes with the crystallization of the wild-type and mutant SH3 domains from chicken src tyrosine kinase. Acta crystallographica. Section D. 57(Pt 5), 759-62. Abstract  Download: kim01A.pdf (274.8 KB)
Kim, D. E., Yi Q., Gladwin S. T., Goldberg J. M., & Baker D. (1998).  The single helix in protein L is largely disrupted at the rate-limiting step in folding. Journal of molecular biology. 284(3), 807-15. Abstract  Download: kim98A.pdf (1.11 MB)
Kim, D. E., Gu H., & Baker D. (1998).  The sequences of small proteins are not extensively optimized for rapid folding by natural selection. Proceedings of the National Academy of Sciences of the United States of America. 95(9), 4982-6. Abstract  Download: kim98A.pdf (220.84 KB)
Kidd, B. A., Baker D., & Thomas W. E. (2009).  Computation of conformational coupling in allosteric proteins. PLoS computational biology. 5(8), e1000484. Abstract  Download: kidd09A.pdf (484.92 KB)
Khersonsky, O., Kiss G., Röthlisberger D., Dym O., Albeck S., Houk K. N., et al. (2012).  Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59.. Proceedings of the National Academy of Sciences of the United States of America. 109(26), 10358-63. Abstract
Khersonsky, O., Röthlisberger D., Wollacott A. M., Murphy P., Dym O., Albeck S., et al. (2011).  Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution. Journal of molecular biology. 407(3), 391-412. Abstract  Download: khersonsky11A.pdf (1.77 MB)
Khatib, F., DiMaio F., Cooper S., Kazmierczyk M., Gilski M., Krzywda S., et al. (2011).  Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nature structural & molecular biology. 18(10), 1175-7. Abstract  Download: khatib11A.pdf (893.7 KB)
Khatib, F., Cooper S., Tyka M. D., Xu K., Makedon I., Popovic Z., et al. (2011).  Algorithm discovery by protein folding game players.. Proceedings of the National Academy of Sciences of the United States of America. Abstract  Download: Khatib11B.pdf (2.4 MB)
Khare, S. D., Kipnis Y., Greisen P. J., Takeuchi R., Ashani Y., Goldsmith M., et al. (2012).  Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. Nature chemical biology. Abstract  Download: khare12A.pdf (1.14 MB)
Kellogg, E. H., Leaver-Fay A., & Baker D. (2011).  Role of conformational sampling in computing mutation-induced changes in protein structure and stability. Proteins. 79(3), 830-8. Abstract  Download: kellogg11A.pdf (430.48 KB)
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
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)
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)