dekim

2011
Leaver-Fay, A., Tyka M., Lewis S. M., Lange O. F., Thompson J., Jacak R., et al. (2011).  ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods in enzymology. 487, 545-74. Abstract  Download: leaver-fay11A.pdf (1.53 MB)
2009
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)
2008
Fan, E., Baker D., Fields S., Gelb M. H., Buckner F. S., Van Voorhis W. C., et al. (2008).  Structural genomics of pathogenic protozoa: an overview. Methods in molecular biology. 426, 497-513. Abstract
2007
Das, R., Qian B., Raman S., Vernon R., Thompson J., Bradley P., et al. (2007).  Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins. 69 Suppl 8, 118-28. Abstract  Download: das07B.pdf (808.02 KB)
2006
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)
2005
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)
Bradley, P., Malmström L., Qian B., Schonbrun J., Chivian D., Kim D. E., et al. (2005).  Free modeling with Rosetta in CASP6. Proteins. 61 Suppl 7, 128-34. Abstract  Download: bradley05A.pdf (1.17 MB)
Chivian, D., Kim D. E., Malmström L., Schonbrun J., Rohl C. A., & Baker D. (2005).  Prediction of CASP6 structures using automated Robetta protocols. Proteins. 61 Suppl 7, 157-66. Abstract  Download: chivian05A.pdf (1.13 MB)
2004
Svensson, H. G., Wedemeyer W. J., Ekstrom J. L., Callender D. R., Kortemme T., Kim D. E., et al. (2004).  Contributions of amino acid side chains to the kinetics and thermodynamics of the bivalent binding of protein L to Ig kappa light chain. Biochemistry. 43(9), 2445-57. Abstract  Download: svensson04A.pdf (522.01 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)
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)
2003
Chivian, D., Kim D. E., Malmström L., Bradley P., Robertson T., Murphy P., et al. (2003).  Automated prediction of CASP-5 structures using the Robetta server. Proteins. 53 Suppl 6, 524-33. Abstract  Download: chivian03A.pdf (501.15 KB)
2002
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)
2001
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)
O'Neill, J. W., Kim D. E., Johnsen K., Baker D., & Zhang K. Y. (2001).  Single-site mutations induce 3D domain swapping in the B1 domain of protein L from Peptostreptococcus magnus. Structure. 9(11), 1017-27. Abstract  Download: o'neill01A.pdf (627.3 KB)
O'Neill, J. W., Kim D. E., Baker D., & Zhang K. Y. (2001).  Structures of the B1 domain of protein L from Peptostreptococcus magnus with a tyrosine to tryptophan substitution.. Acta crystallographica. Section D, Biological crystallography. 57(Pt 4), 480-7. Abstract
2000
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)
1999
Gu, H., Doshi N., Kim D. E., Simons K. T., Santiago J. V., Nauli S., et al. (1999).  Robustness of protein folding kinetics to surface hydrophobic substitutions. Protein science. 8(12), 2734-41. Abstract  Download: gu99A.pdf (368.14 KB)
1998
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)
1997
Gu, H., Kim D. E., & Baker D. (1997).  Contrasting roles for symmetrically disposed beta-turns in the folding of a small protein. Journal of molecular biology. 274(4), 588-96. Abstract  Download: gu97A.pdf (654.1 KB)