Publications

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Eiben, C. B., Siegel J. B., Bale J. B., Cooper S., Khatib F., Shen B. W., et al. (2012).  Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nature biotechnology. 30(2), 190-2. Abstract  Download: eiben12A.pdf (552.17 KB)
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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
Fleishman, S. J., & Baker D. (2012).  Role of the biomolecular energy gap in protein design, structure, and evolution.. Cell. 149(2), 262-73. Abstract
Fleishman, S. J., Khare S. D., Koga N., & Baker D. (2011).  Restricted sidechain plasticity in the structures of native proteins and complexes. Protein science. 20(4), 753-7. Abstract  Download: fleishman11A.pdf (295.85 KB)
Fleishman, S. J., Whitehead T. A., Ekiert D. C., Dreyfus C., Corn J. E., Strauch E. - M., et al. (2011).  Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science. 332(6031), 816-21. Abstract  Download: fleishman11B.pdf (643.74 KB)
Fowler, D. M., Araya C. L., Fleishman S. J., Kellogg E. H., Stephany J. J., Baker D., et al. (2010).  High-resolution mapping of protein sequence-function relationships. Nature methods. 7(9), 741-6. Abstract  Download: fowler10A.pdf (1.09 MB)
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Goobes, G., Goobes R., Shaw W. J., Gibson J. M., Long J. R., Raghunathan V., et al. (2008).  The structure, dynamics, and energetics of protein adsorption-lessons learned from adsorption of statherin to hydroxyapatite. Magnetic resonance in chemistry. 45(S1), S32-S47. Abstract  Download: goobes08A.pdf (523.71 KB)
Goobes, G., Goobes R., Schueler-Furman O., Baker D., Stayton P. S., & Drobny G. P. (2006).  Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals. Proceedings of the National Academy of Sciences of the United States of America. 103(44), 16083-8. Abstract  Download: goobes06A.pdf (725.15 KB)
Graña, O., Baker D., MacCallum R. M., Meiler J., Punta M., Rost B., et al. (2005).  CASP6 assessment of contact prediction. Proteins. 61 Suppl 7, 214-24. Abstract  Download: grana05A.pdf (857.44 KB)
Grantcharova, V. P., & Baker D. (1997).  Folding dynamics of the src SH3 domain. Biochemistry. 36(50), 15685-92. Abstract  Download: grantcharova97A.pdf (171.64 KB)
Grantcharova, V. P., & Baker D. (2001).  Circularization changes the folding transition state of the src SH3 domain. Journal of molecular biology. 306(3), 555-63. Abstract  Download: grantcharova01A.pdf (341.23 KB)
Grantcharova, V. P., Riddle D. S., & Baker D. (2000).  Long-range order in the src SH3 folding transition state. Proceedings of the National Academy of Sciences of the United States of America. 97(13), 7084-9. Abstract  Download: grantcharova00A.pdf (313 KB)
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
Grantcharova, V. P., Riddle D. S., Santiago J. V., & Baker D. (1998).  Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain. Nature structural biology. 5(8), 714-20. Abstract  Download: grantcharova98A.pdf (833.81 KB)
Gray, J. J., Moughon S., Wang C., Schueler-Furman O., Kuhlman B., Rohl C. A., et al. (2003).  Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. Journal of molecular biology. 331(1), 281-99. Abstract  Download: gray03A.pdf (2.12 MB)
Gray, J. J., Moughon S. E., Kortemme T., Schueler-Furman O., Misura K. M. S., Morozov A. V., et al. (2003).  Protein-protein docking predictions for the CAPRI experiment. Proteins. 52(1), 118-22. Abstract  Download: gray03B.pdf (467.92 KB)
Gu, H., Yi Q., Bray S. T., Riddle D. S., Shiau A. K., & Baker D. (1995).  A phage display system for studying the sequence determinants of protein folding. Protein science. 4(6), 1108-17. Abstract  Download: gu95A.pdf (4.61 MB)
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)
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)
Guenaga, J., Dosenovic P., Ofek G., Baker D., Schief W. R., Kwong P. D., et al. (2011).  Heterologous epitope-scaffold prime:boosting immuno-focuses B cell responses to the HIV-1 gp41 2F5 neutralization determinant. PloS one. 6(1), e16074. Abstract  Download: guenaga11A.pdf (1.95 MB)
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Han, K. F., Bystroff C., & Baker D. (1997).  Three-dimensional structures and contexts associated with recurrent amino acid sequence patterns. Protein science. 6(7), 1587-90. Abstract  Download: han97A.pdf (2.35 MB)
Han, K. F., & Baker D. (1995).  Recurring local sequence motifs in proteins. Journal of molecular biology. 251(1), 176-87. Abstract  Download: han95A.pdf (297.22 KB)
Han, K. F., & Baker D. (1996).  Global properties of the mapping between local amino acid sequence and local structure in proteins. Proceedings of the National Academy of Sciences of the United States of America. 93(12), 5814-8. Abstract  Download: han96A.pdf (938.22 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)
Havranek, J. J., Duarte C. M., & Baker D. (2004).  A simple physical model for the prediction and design of protein-DNA interactions. Journal of molecular biology. 344(1), 59-70. Abstract  Download: havranek04A.pdf (445.63 KB)
Hazbun, T. R., Malmström L., Anderson S., Graczyk B. J., Fox B., Riffle M., et al. (2003).  Assigning function to yeast proteins by integration of technologies. Molecular cell. 12(6), 1353-65. Abstract  Download: hazbun03A.pdf (390.65 KB)
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Ivankov, D. N., Garbuzynskiy S. O., Alm E., Plaxco K. W., Baker D., & Finkelstein A. V. (2003).  Contact order revisited: influence of protein size on the folding rate. Protein science. 12(9), 2057-62. Abstract  Download: ivankov03A.pdf (146.63 KB)
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Jiang, L., Althoff E. A., Clemente F. R., Doyle L., Röthlisberger D., Zanghellini A., et al. (2008).  De novo computational design of retro-aldol enzymes. Science. 319(5868), 1387-91. Abstract  Download: jiang08A.pdf (629.34 KB)
Jiang, L., Kuhlman B., Kortemme T., & Baker D. (2005).  A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins. 58(4), 893-904. Abstract  Download: jiang05A.pdf (723.29 KB)
Joachimiak, L. A., Kortemme T., Stoddard B. L., & Baker D. (2006).  Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface. Journal of molecular biology. 361(1), 195-208. Abstract  Download: joachimiak06A.pdf (1.04 MB)
Johnsen, K., O'Neill J. W., Kim D. E., Baker D., & Zhang K. Y. (2000).  Crystallization and preliminary X-ray diffraction studies of mutants of B1 IgG-binding domain of protein L from Peptostreptococcus magnus. Acta crystallographica. Section D. 56(Pt 4), 506-8. Abstract  Download: johnsen00A.pdf (244.36 KB)
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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)
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)
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
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)
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)
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)
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)
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
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)
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, 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., 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)
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, 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., 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., 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)
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)
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)
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)
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)
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)
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)
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., 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., 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., & 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)
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)
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)
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)
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)
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)
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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)
Lange, O. F., Rossi P., Sgourakis N. G., Song Y., Lee H. - W., Aramini J. M., et al. (2012).  Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples.. Proceedings of the National Academy of Sciences of the United States of America. 109(27), 10873-8. Abstract
Lange, O. F., & Baker D. (2012).  Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation.. Proteins. 80(3), 884-95. Abstract
Larson, S. M., Ruczinski I., Davidson A. R., Baker D., & Plaxco K. W. (2002).  Residues participating in the protein folding nucleus do not exhibit preferential evolutionary conservation. Journal of molecular biology. 316(2), 225-33. Abstract  Download: larson02A.pdf (213.29 KB)
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)
Lee, M. R., Baker D., & Kollman P. A. (2001).  2.1 and 1.8 A average C(alpha) RMSD structure predictions on two small proteins, HP-36 and s15. Journal of the American Chemical Society. 123(6), 1040-6. Abstract  Download: lee01A.pdf (180.46 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)
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)
Li, M., DiMaio F., Zhou D., Gustchina A., Lubkowski J., Dauter Z., et al. (2011).  Crystal structure of XMRV protease differs from the structures of other retropepsins. Nature structural & molecular biology. 18(2), 227-9. Abstract  Download: li11A.pdf (663.49 KB)
Li, J., Shinjo M., Matsumura Y., Morita M., Baker D., Ikeguchi M., et al. (2007).  An alpha-helical burst in the src SH3 folding pathway. Biochemistry. 46(17), 5072-82. Abstract  Download: li07A.pdf (493.42 KB)
Liu, L., Murphy P., Baker D., & Lutz S. (2010).  Computational design of orthogonal nucleoside kinases. Chemical communications. 46(46), 8803-5. Abstract  Download: liu10A.pdf (1.22 MB)
Loquet, A., Sgourakis N. G., Gupta R., Giller K., Riedel D., Goosmann C., et al. (2012).  Atomic model of the type III secretion system needle. Nature. Abstract  Download: sgourakis12A.pdf (1015.62 KB)
Luo, B. - H., Karanicolas J., Harmacek L. D., Baker D., & Springer T. A. (2009).  Rationally designed integrin beta3 mutants stabilized in the high affinity conformation. The Journal of biological chemistry. 284(6), 3917-24. Abstract  Download: luo09A.pdf (673.21 KB)
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Malmström, L., Riffle M., Strauss C. E. M., Chivian D., Davis T. N., Bonneau R., et al. (2007).  Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS biology. 5(4), e76. Abstract  Download: malmström07A.pdf (592.42 KB)
McBeth, C., Seamons A., Pizarro J. C., Fleishman S. J., Baker D., Kortemme T., et al. (2008).  A new twist in TCR diversity revealed by a forbidden alphabeta TCR. Journal of molecular biology. 375(5), 1306-19. Abstract  Download: mcbeth08A.pdf (5.02 MB)