Publications

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A
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)
Alm, E., Morozov A. V., Kortemme T., & Baker D. (2002).  Simple physical models connect theory and experiment in protein folding kinetics. Journal of molecular biology. 322(2), 463-76. Abstract  Download: alm02A.pdf (1.2 MB)
Alm, E., & Baker D. (1999).  Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proceedings of the National Academy of Sciences of the United States of America. 96(20), 11305-10. Abstract  Download: alm99A.pdf (574.66 KB)
Alm, E., & Baker D. (1999).  Matching theory and experiment in protein folding.. Current opinion in structural biology. 9(2), 189-96. Abstract
Althoff, E. A., Wang L., Jiang L., Giger L., Lassila J. K., Wang Z., et al. (2012).  Robust design and optimization of retroaldol enzymes.. Protein science : a publication of the Protein Society. 21(5), 717-26. Abstract
André, I., Bradley P., Wang C., & Baker D. (2007).  Prediction of the structure of symmetrical protein assemblies. Proceedings of the National Academy of Sciences of the United States of America. 104(45), 17656-61. Abstract  Download: André07A.pdf (1.15 MB)
André, I., Strauss C. E. M., Kaplan D. B., Bradley P., & Baker D. (2008).  Emergence of symmetry in homooligomeric biological assemblies. Proceedings of the National Academy of Sciences of the United States of America. 105(42), 16148-52. Abstract  Download: andré08A.pdf (588.8 KB)
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)
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)
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)
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)
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)
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)
B
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)
Baker, D., Wuestehube L., Schekman R., Botstein D., & Segev N. (1990).  GTP-binding Ypt1 protein and Ca2+ function independently in a cell-free protein transport reaction. Proceedings of the National Academy of Sciences of the United States of America. 87(1), 355-9. Abstract  Download: baker90A.pdf (1020.83 KB)
Baker, D., Silen J. L., & Agard D. A. (1992).  Protease pro region required for folding is a potent inhibitor of the mature enzyme. Proteins. 12(4), 339-44. Abstract
Baker, D., Krukowski A. E., & Agard D. A. (1993).  Uniqueness and the ab initio phase problem in macromolecular crystallography. Acta crystallographica. Section D. 49(Pt 1), 186-92. Abstract  Download: baker93C.pdf (803.27 KB)
Baker, D. (2010).  An exciting but challenging road ahead for computational enzyme design. Protein science.  Download: baker10A.pdf (58.56 KB)
Baker, D., Hicke L., Rexach M., Schleyer M., & Schekman R. (1988).  Reconstitution of SEC gene product-dependent intercompartmental protein transport. Cell. 54(3), 335-44. Abstract  Download: baker88.pdf (3.33 MB)
Baker, D. (2006).  Prediction and design of macromolecular structures and interactions. Philosophical transactions of the Royal Society of London. 361(1467), 459-63. Abstract  Download: baker06A.pdf (688.82 KB)
Baker, D., Sohl J. L., & Agard D. A. (1992).  A protein-folding reaction under kinetic control. Nature. 356(6366), 263-5. Abstract  Download: baker92A.pdf (384.94 KB)
Baker, D., & Sali A. (2001).  Protein structure prediction and structural genomics.. Science (New York, N.Y.). 294(5540), 93-6. Abstract
Baker, D., Bystroff C., Fletterick R. J., & Agard D. A. (1993).  PRISM: topologically constrained phased refinement for macromolecular crystallography. Acta crystallographica. Section D. 49(Pt 5), 429-39. Abstract  Download: baker93A.pdf (3.87 MB)
Baker, D. (1998).  Metastable states and folding free energy barriers.. Nature structural biology. 5(12), 1021-4.
Baker, D. (2000).  A surprising simplicity to protein folding. Nature. 405(6782), 39-42. Abstract  Download: baker00A.pdf (853.11 KB)
Baker, D., & DeGrado W. F. (1999).  Engineering and design. Current opinion in structural biology. 9(4), 485-6.
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)
Barth, P., Wallner B., & Baker D. (2009).  Prediction of membrane protein structures with complex topologies using limited constraints. Proceedings of the National Academy of Sciences of the United States of America. 106(5), 1409-14. Abstract  Download: barth09A.pdf (596.08 KB)
Barth, P., Schonbrun J., & Baker D. (2007).  Toward high-resolution prediction and design of transmembrane helical protein structures. Proceedings of the National Academy of Sciences of the United States of America. 104(40), 15682-7. Abstract  Download: barth07A.pdf (728.74 KB)
Baxter, S., Lambert A. R., Kuhar R., Jarjour J., Kulshina N., Parmeggiani F., et al. (2012).  Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases.. Nucleic acids research. 40(16), 7985-8000. Abstract
Blum, B., Jordan M. I., & Baker D. (2010).  Feature space resampling for protein conformational search. Proteins. 78(6), 1583-93. Abstract  Download: blum10A.pdf (621.02 KB)
Bonneau, R., & Baker D. (2001).  Ab initio protein structure prediction: progress and prospects.. Annual review of biophysics and biomolecular structure. 30, 173-89. Abstract
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)
Bonneau, R., Strauss C. E., & Baker D. (2001).  Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation. Proteins. 43(1), 1-11. Abstract  Download: bonneau01A.pdf (554.67 KB)
Bonneau, R., Tsai J., Ruczinski I., & Baker D. (2001).  Functional inferences from blind ab initio protein structure predictions. Journal of structural biology. 134(2-3), 186-90. Abstract  Download: bonneau01B.pdf (115.55 KB)
Bonneau, R., Strauss C. E. M., Rohl C. A., Chivian D., Bradley P., Malmström L., et al. (2002).  De novo prediction of three-dimensional structures for major protein families. Journal of molecular biology. 322(1), 65-78. Abstract  Download: bonneau02B.pdf (855.42 KB)
Bonneau, R., Tsai J., Ruczinski I., Chivian D., Rohl C., Strauss C. E., et al. (2001).  Rosetta in CASP4: progress in ab initio protein structure prediction. Proteins. Suppl 5, 119-26. Abstract  Download: bonneau01C.pdf (682.51 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)
Bouvignies, G., Vallurupalli P., Hansen F. D., Correia B. E., Lange O., Bah A., et al. (2011).  Solution structure of a minor and transiently formed state of a T4 lysozyme mutant. Nature. 477(7362), 111-4. Abstract  Download: bouvignies11A.pdf (1023.45 KB)
Bowers, P. M., Strauss C. E., & Baker D. (2000).  De novo protein structure determination using sparse NMR data.. Journal of biomolecular NMR. 18(4), 311-8. Abstract
Bradley, P., Misura K. M. S., & Baker D. (2005).  Toward high-resolution de novo structure prediction for small proteins. Science. 309(5742), 1868-71. Abstract  Download: bradley05B.pdf (421.25 KB)
Bradley, P., Chivian D., Meiler J., Misura K. M. S., Rohl C. A., Schief W. R., et al. (2003).  Rosetta predictions in CASP5: successes, failures, and prospects for complete automation. Proteins. 53 Suppl 6, 457-68. Abstract  Download: bradley03A.pdf (1.05 MB)
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)
Bradley, P., & Baker D. (2006).  Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation. Proteins. 65(4), 922-9. Abstract  Download: bradley06A.pdf (837.59 KB)
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)
Bystroff, C., Thorsson V., & Baker D. (2000).  HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins. Journal of molecular biology. 301(1), 173-90. Abstract  Download: bystroff00A.pdf (730.85 KB)
Bystroff, C., Baker D., Fletterick R. J., & Agard D. A. (1993).  PRISM: application to the solution of two protein structures. Acta crystallographica. Section D. 49(Pt 5), 440-8. Abstract  Download: bystroff93A.pdf (1.05 MB)
Bystroff, C., & Baker D. (1998).  Prediction of local structure in proteins using a library of sequence-structure motifs. Journal of molecular biology. 281(3), 565-77. Abstract  Download: bystroff98A.pdf (1.76 MB)
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)
Bystroff, C., Simons K. T., Han K. F., & Baker D. (1996).  Local sequence-structure correlations in proteins. Current opinion in biotechnology. 7(4), 417-21. Abstract  Download: bystroff96A.pdf (518.77 KB)
C
Chen, Y., Kortemme T., Robertson T., Baker D., & Varani G. (2004).  A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys. Nucleic acids research. 32(17), 5147-62. Abstract  Download: chen04.pdf (1.47 MB)
Chen, D. - H., Baker M. L., Hryc C. F., DiMaio F., Jakana J., Wu W., et al. (2011).  Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus. Proceedings of the National Academy of Sciences of the United States of America. 108(4), 1355-60. Abstract  Download: chen11A.pdf (2.71 MB)
Cheng, G., Qian B., Samudrala R., & Baker D. (2005).  Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design. Nucleic acids research. 33(18), 5861-7. Abstract  Download: cheng05A.pdf (507.13 KB)
Chevalier, B. S., Kortemme T., Chadsey M. S., Baker D., Monnat R. J., & Stoddard B. L. (2002).  Design, activity, and structure of a highly specific artificial endonuclease. Molecular cell. 10(4), 895-905. Abstract  Download: chevalier02A.pdf (671.2 KB)
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)
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)
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)
Chivian, D., & Baker D. (2006).  Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. Nucleic acids research. 34(17), e112. Abstract  Download: chivian06A.pdf (1.95 MB)
Cho, H. D., Sood V. D., Baker D., & Weiner A. M. (2008).  On the role of a conserved, potentially helix-breaking residue in the tRNA-binding alpha-helix of archaeal CCA-adding enzymes. RNA. 14(7), 1284-9. Abstract  Download: cho08A.pdf (209.43 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)
Cooper, S., Khatib F., Treuille A., Barbero J., Lee J., Beenen M., et al. (2010).  Predicting protein structures with a multiplayer online game. Nature. 466(7307), 756-60. Abstract  Download: cooper10A.pdf (1.33 MB)
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)
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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)
Dantas, G., Watters A. L., Lunde B. M., Eletr Z. M., Isern N. G., Roseman T., et al. (2006).  Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution. Journal of molecular biology. 362(5), 1004-24. Abstract  Download: dantas06A.pdf (1.15 MB)
Dantas, G., Kuhlman B., Callender D., Wong M., & Baker D. (2003).  A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. Journal of molecular biology. 332(2), 449-60. Abstract  Download: dantas03A.pdf (1.96 MB)
Dantas, G., Corrent C., Reichow S. L., Havranek J. J., Eletr Z. M., Isern N. G., et al. (2007).  High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design. Journal of molecular biology. 366(4), 1209-21. Abstract  Download: dantas07A.pdf (1.71 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)
Das, R., & Baker D. (2009).  Prospects for de novo phasing with de novo protein models. Acta crystallographica. 65(Pt 2), 169-75. Abstract  Download: das09B.pdf (713.43 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. (2008).  Macromolecular modeling with rosetta. Annual review of biochemistry. 77, 363-82. Abstract  Download: das08A.pdf (1.13 MB)
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)
Das, R., André I., Shen Y., Wu Y., Lemak A., Bansal S., et al. (2009).  Simultaneous prediction of protein folding and docking at high resolution. Proceedings of the National Academy of Sciences of the United States of America. 106(45), 18978-83. Abstract  Download: das09A.pdf (1.57 MB)
Das, R., Kudaravalli M., Jonikas M., Laederach A., Fong R., Schwans J. P., et al. (2008).  Structural inference of native and partially folded RNA by high-throughput contact mapping. Proceedings of the National Academy of Sciences of the United States of America. 105(11), 4144-9. Abstract  Download: das08A.pdf (806.02 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)
Davis, I. W., & Baker D. (2009).  RosettaLigand docking with full ligand and receptor flexibility. Journal of molecular biology. 385(2), 381-92. Abstract  Download: davis09B.pdf (1.36 MB)
Dietrich, J. A., Yoshikuni Y., Fisher K. J., Woolard F. X., Ockey D., McPhee D. J., et al. (2009).  A novel semi-biosynthetic route for artemisinin production using engineered substrate-promiscuous P450(BM3). ACS chemical biology. 4(4), 261-7. Abstract  Download: dietrich09A.pdf (1.67 MB)
DiMaio, F., Tyka M. D., Baker M. L., Chiu W., & Baker D. (2009).  Refinement of protein structures into low-resolution density maps using rosetta. Journal of molecular biology. 392(1), 181-90. Abstract  Download: dimaio09A.pdf (1.54 MB)
DiMaio, F., Terwilliger T. C., Read R. J., Wlodawer A., Oberdorfer G., Wagner U., et al. (2011).  Improved molecular replacement by density- and energy-guided protein structure optimization. Nature. Abstract  Download: dimaio11A.pdf (972.77 KB)
Dobson, N., Dantas G., Baker D., & Varani G. (2006).  High-resolution structural validation of the computational redesign of human U1A protein. Structure. 14(5), 847-56. Abstract  Download: dobson06A.pdf (448.74 KB)
Doyle, R., Simons K., Qian H., & Baker D. (1997).  Local interactions and the optimization of protein folding. Proteins. 29(3), 282-91. Abstract  Download: doyle97A.pdf (161.67 KB)