Publications

Sort by: [ Author (Desc)] Title Type Year
Filters: First Letter Of Last Name is B  [Clear All Filters]
A [B] C D E F G H I J K L M N O P Q R S T U V W X Y Z   [Show ALL]
B
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)
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)
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)
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., 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)
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
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)
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)
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)
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)
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)
Bjelic, S., Nivón L. G., Çelebi-Ölçüm N., Kiss G., Rosewall C. F., Lovick H. M., et al. (2013).  Computational design of enone-binding proteins with catalytic activity for the Morita-Baylis-Hillman reaction.. ACS chemical biology. 8(4), 749-57. Abstract
Bergeron, J. R. C., Worrall L. J., Sgourakis N. G., DiMaio F., Pfuetzner R. A., Felise H. B., et al. (2013).  A Refined Model of the Prototypical Salmonella SPI-1 T3SS Basal Body Reveals the Molecular Basis for Its Assembly.. PLoS pathogens. 9(4), e1003307. Abstract
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
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)
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)
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)
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)