Publications

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Journal Article
Minard, P., Scalley-Kim M., Watters A., & Baker D. (2001).  A "loop entropy reduction" phage-display selection for folded amino acid sequences. Protein science. 10(1), 129-34. Abstract  Download: minard01A.pdf (229.21 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)
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)
Thompson, M. J., Sievers S. A., Karanicolas J., Ivanova M. I., Baker D., & Eisenberg D. (2006).  The 3D profile method for identifying fibril-forming segments of proteins. Proceedings of the National Academy of Sciences of the United States of America. 103(11), 4074-8. Abstract  Download: thompson06A.pdf (738.97 KB)
Ban, Y. A., Correia B. E., Holmes M., Boni E., Sather N., Bretz C., et al. (2009).  4e10 epitope-scaffolds mimic the antibody-bound epitope conformation and block neutralization by sera from rare HIV+ individuals. Retrovirology. 6,  Download: ban09A.pdf (130.41 KB)
Chivian, D., Robertson T., Bonneau R., & Baker D. (2003).  Ab initio methods. Methods of biochemical analysis. 44, 547-57. Download: chivan03A.pdf (5.89 MB)
Baker, M. L., Jiang W., Wedemeyer W. J., Rixon F. J., Baker D., & Chiu W. (2006).  Ab initio modeling of the herpesvirus VP26 core domain assessed by CryoEM density. PLoS computational biology. 2(10), e146. Abstract  Download: baker06B.pdf (945.92 KB)
Simons, K. T., Bonneau R., Ruczinski I., & Baker D. (1999).  Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins. Suppl 3, 171-6. Abstract
Bonneau, R., & Baker D. (2001).  Ab initio protein structure prediction: progress and prospects.. Annual review of biophysics and biomolecular structure. 30, 173-89. Abstract
Raman, S., Huang Y. J., Mao B., Rossi P., Aramini J. M., Liu G., et al. (2010).  Accurate automated protein NMR structure determination using unassigned NOESY data. Journal of the American Chemical Society. 132(1), 202-7. Abstract  Download: raman10A.pdf (3.49 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)
Thompson, J. M., Sgourakis N. G., Liu G., Rossi P., Tang Y., Mills J. L., et al. (2012).  Accurate protein structure modeling using sparse NMR data and homologous structure information.. Proceedings of the National Academy of Sciences of the United States of America. 109(25), 9875-80. Abstract
Brzovic, P. S., Heikaus C. C., Kisselev L., Vernon R., Herbig E., Pacheco D., et al. (2011).  The acidic transcription activator Gcn4 binds the mediator subunit Gal11/Med15 using a simple protein interface forming a fuzzy complex. Molecular cell. 44(6), 942-53. Abstract  Download: brzovic11A.pdf (1.14 MB)
S, R., B Q., D B., & RC W. (2008).  Advances in Rosetta Protein Structure Prediction on Massively Parallel Systems. Journal of Research and Development . 52(1-2):7-17, Abstract  Download: raman08A.pdf (446.3 KB)
Schlosshauer, M., & Baker D. (2002).  Ageneral expressionforbimolecularassociationrates withorientational constraints. Physical Chemistry B.  Download: schlosshauer02A.pdf (250.05 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)
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)
Murphy, P. M., Bolduc J. M., Gallaher J. L., Stoddard B. L., & Baker D. (2009).  Alteration of enzyme specificity by computational loop remodeling and design. Proceedings of the National Academy of Sciences of the United States of America. 106(23), 9215-20. Abstract  Download: murphy09A.pdf (954.03 KB)
Tyka, M. D., Keedy D. A., André I., DiMaio F., Song Y., Richardson D. C., et al. (2010).  Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping. Journal of molecular biology. Abstract  Download: tyka10A.pdf (2.13 MB)
Misura, K. M. S., Morozov A. V., & Baker D. (2004).  Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction. Journal of molecular biology. 342(2), 651-64. Abstract  Download: misura04A.pdf (867.48 KB)
Simons, K. T., Kooperberg C., Huang E., & Baker D. (1997).  Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. Journal of molecular biology. 268(1), 209-25. Abstract  Download: simons97A.pdf (769.01 KB)
Tress, M., Cheng J., Baldi P., Joo K., Lee J., Seo J. - H., et al. (2007).  Assessment of predictions submitted for the CASP7 domain prediction category. Proteins. 69 Suppl 8, 137-51. Abstract  Download: tress07A.pdf (1.5 MB)
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)
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)
Das, R., Karanicolas J., & Baker D. (2010).  Atomic accuracy in predicting and designing noncanonical RNA structure. Nature methods. 7(4), 291-4. Abstract  Download: das10A.pdf (1.13 MB)
Das, R., & Baker D. (2007).  Automated de novo prediction of native-like RNA tertiary structures. Proceedings of the National Academy of Sciences of the United States of America. 104(37), 14664-9. Abstract  Download: das07A.pdf (1.29 MB)
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)
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)
Davis, I. W., Raha K., Head M. S., & Baker D. (2009).  Blind docking of pharmaceutically relevant compounds using RosettaLigand. Protein science. 18(9), 1998-2002. Abstract  Download: davis09A.pdf (261.62 KB)
Bystroff, C., & Baker D. (1997).  Blind predictions of local protein structure in CASP2 targets using the I-sites library. Proteins. Suppl 1, 167-71. Abstract  Download: bystroff97A.pdf (230.61 KB)
Rosato, A., Aramini J. M., Arrowsmith C., Bagaria A., Baker D., Cavalli A., et al. (2012).  Blind testing of routine, fully automated determination of protein structures from NMR data. Structure. 20(2), 227-36. Abstract
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)
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
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)
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)
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)