Publications

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Palmer, A. E., Giacomello M., Kortemme T., Hires A. S., Lev-Ram V., Baker D., et al. (2006).  Ca2+ indicators based on computationally redesigned calmodulin-peptide pairs. Chemistry & biology. 13(5), 521-30. Abstract  Download: palmer06A.pdf (591.03 KB)
Rosato, A., Bagaria A., Baker D., Bardiaux B., Cavalli A., Doreleijers J. F., et al. (2009).  CASD-NMR: critical assessment of automated structure determination by NMR. Nature methods. 6(9), 625-6. Download: rosato09A.pdf (175.47 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)
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)
Plaxco, K. W., Millett I. S., Segel D. J., Doniach S., & Baker D. (1999).  Chain collapse can occur concomitantly with the rate-limiting step in protein folding. Nature structural biology. 6(6), 554-6. Abstract  Download: plaxco99A.pdf (474.01 KB)
Cooper, S., Treuille A., Barbero J., Leaver-Fay A., Tuite K., Khatib F., et al. (2010).  The Challenge of Designing Scientific Discovery Games. Proceedings of the Fifth international Conference on the Foundations of Digital Games. Abstract  Download: cooper10A.pdf (1.19 MB)
Scalley-Kim, M., & Baker D. (2004).  Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection. Journal of molecular biology. 338(3), 573-83. Abstract  Download: scalley-kim04A.pdf (537.27 KB)
Yi, Q., Scalley M. L., Simons K. T., Gladwin S. T., & Baker D. (1997).  Characterization of the free energy spectrum of peptostreptococcal protein L. Folding & design. 2(5), 271-80. Abstract  Download: yi97A.pdf (188.99 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)
Morozov, A. V., Kortemme T., Tsemekhman K., & Baker D. (2004).  Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proceedings of the National Academy of Sciences of the United States of America. 101(18), 6946-51. Abstract  Download: morozov04A.pdf (444.99 KB)
Shortle, D., Simons K. T., & Baker D. (1998).  Clustering of low-energy conformations near the native structures of small proteins. Proceedings of the National Academy of Sciences of the United States of America. 95(19), 11158-62. Abstract  Download: shortle98A.pdf (243.13 KB)
Muratore, K. E., Seeliger M. A., Wang Z., Fomina D., Neiswinger J., Havranek J. J., et al. (2009).  Comparative analysis of mutant tyrosine kinase chemical rescue. Biochemistry. 48(15), 3378-86. Abstract  Download: muratore09A.pdf (318.66 KB)
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)
Ulge, U. Y., Baker D. A., & Monnat R. J. (2011).  Comprehensive computational design of mCreI homing endonuclease cleavage specificity for genome engineering. Nucleic acids research. Abstract  Download: ulge11A.pdf (638.72 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)
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)
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)
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)
Siegel, J. B., Zanghellini A., Lovick H. M., Kiss G., Lambert A. R., St Clair J. L., et al. (2010).  Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science. 329(5989), 309-13. Abstract  Download: siegel10A.pdf (1.55 MB)
Richter, F., Blomberg R., Khare S. D., Kiss G., Kuzin A. P., Smith A. J. T., et al. (2012).  Computational design of catalytic dyads and oxyanion holes for ester hydrolysis.. Journal of the American Chemical Society. 134(39), 16197-206. Abstract
Correia, B. E., Ban Y. - E. A., Holmes M. A., Xu H., Ellingson K., Kraft Z., et al. (2010).  Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope. Structure. 18(9), 1116-26. Abstract  Download: correia10A.pdf (1.12 MB)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
Nauli, S., Kuhlman B., & Baker D. (2001).  Computer-based redesign of a protein folding pathway.. Nature structural biology. 8(7), 602-5. Abstract  Download: nauli01A.pdf (1.39 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)
Schueler-Furman, O., & Baker D. (2003).  Conserved residue clustering and protein structure prediction. Proteins. 52(2), 225-35. Abstract  Download: schueler-furman03A.pdf (245.13 KB)
Spreter, T., Yip C. K., Sanowar S., André I., Kimbrough T. G., Vuckovic M., et al. (2009).  A conserved structural motif mediates formation of the periplasmic rings in the type III secretion system. Nature structural & molecular biology. 16(5), 468-76. Abstract  Download: spreter09A.pdf (2.37 MB)
Shen, Y., Lange O., Delaglio F., Rossi P., Aramini J. M., Liu G., et al. (2008).  Consistent blind protein structure generation from NMR chemical shift data. Proceedings of the National Academy of Sciences of the United States of America. 105(12), 4685-90. Abstract  Download: shen08A.pdf (1.01 MB)
Bonneau, R., Ruczinski I., Tsai J., & Baker D. (2002).  Contact order and ab initio protein structure prediction. Protein science. 11(8), 1937-44. Abstract  Download: bonneau02A.pdf (259.2 KB)
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)
Plaxco, K. W., Simons K. T., & Baker D. (1998).  Contact order, transition state placement and the refolding rates of single domain proteins. Journal of molecular biology. 277(4), 985-94. Abstract  Download: plaxco98B.pdf (304.37 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)
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)
Rank, J. A., & Baker D. (1998).  Contributions of solvent-solvent hydrogen bonding and van der Waals interactions to the attraction between methane molecules in water. Biophysical chemistry. 71(2-3), 199-204. Abstract  Download: rank98A.pdf (120.64 KB)
Boulanger, M. J., Bankovich A. J., Kortemme T., Baker D., & Garcia C. K. (2003).  Convergent mechanisms for recognition of divergent cytokines by the shared signaling receptor gp130. Molecular cell. 12(3), 577-89. Abstract  Download: boulanger03A.pdf (784.25 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)
Tsemekhman, K., Goldschmidt L., Eisenberg D., & Baker D. (2007).  Cooperative hydrogen bonding in amyloid formation. Protein science. 16(4), 761-4. Abstract  Download: tsemekhman07A.pdf (260.96 KB)
D, B., HS C., & KA D. (1993).  Coordinate-Space Formulation of Polymer Lattice Cluster Theory. Journal of Chemical Physics .  Download: baker93B.pdf (960.07 KB)
Meiler, J., & Baker D. (2003).  Coupled prediction of protein secondary and tertiary structure. Proceedings of the National Academy of Sciences of the United States of America. 100(21), 12105-10. Abstract  Download: meiler03A.pdf (618.84 KB)
McCallister, E. L., Alm E., & Baker D. (2000).  Critical role of beta-hairpin formation in protein G folding. Nature structural biology. 7(8), 669-73. Abstract  Download: mccallister00A.pdf (785.9 KB)
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)
Sprague, E. R., Wang C., Baker D., & Bjorkman P. J. (2006).  Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging. PLoS biology. 4(6), e148. Abstract  Download: sprague06A.pdf (539.35 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)
Nauli, S., Kuhlman B., Le Trong I., Stenkamp R. E., Teller D., & Baker D. (2002).  Crystal structures and increased stabilization of the protein G variants with switched folding pathways NuG1 and NuG2. Protein science. 11(12), 2924-31. Abstract  Download: nauli02A.pdf (257.77 KB)
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)