Publications

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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. (1998).  Metastable states and folding free energy barriers.. Nature structural biology. 5(12), 1021-4.
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. (2000).  A surprising simplicity to protein folding. Nature. 405(6782), 39-42. Abstract  Download: baker00A.pdf (853.11 KB)
Baker, D., & Sali A. (2001).  Protein structure prediction and structural genomics.. Science (New York, N.Y.). 294(5540), 93-6. Abstract
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., 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., 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. (2010).  An exciting but challenging road ahead for computational enzyme design. Protein science.  Download: baker10A.pdf (58.56 KB)
Baker, D., & DeGrado W. F. (1999).  Engineering and design. Current opinion in structural biology. 9(4), 485-6.
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, 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. (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)
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., 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)
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)
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., 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)
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., & Baker D. (2001).  Ab initio protein structure prediction: progress and prospects.. Annual review of biophysics and biomolecular structure. 30, 173-89. Abstract
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., 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)
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., 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)
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., 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)
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., 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)
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., 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., 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. (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)