Publications

Sort by: Author [ Title (Asc)] Type Year
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 
R
Ruohola, H., Bremer K. A., Baker D., Swedlow J. R., Jan L. Y., & Jan Y. N. (1991).  Role of neurogenic genes in establishment of follicle cell fate and oocyte polarity during oogenesis in Drosophila.. Cell. 66(3), 433-49. Abstract  Download: ruoholaa91.pdf (0 bytes)
Fleishman, S. J., & Baker D. (2012).  Role of the biomolecular energy gap in protein design, structure, and evolution.. Cell. 149(2), 262-73. Abstract
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)
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)
Leaver-Fay, A., Tyka M., Lewis S. M., Lange O. F., Thompson J., Jacak R., et al. (2011).  ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods in enzymology. 487, 545-74. Abstract  Download: leaver-fay11A.pdf (1.53 MB)
Wang, C., Schueler-Furman O., Andre I., London N., Fleishman S. J., Bradley P., et al. (2007).  RosettaDock in CAPRI rounds 6-12. Proteins. 69(4), 758-63. Abstract  Download: wang07B.pdf (214.39 KB)
Sheffler, W., & Baker D. (2010).  RosettaHoles2: a volumetric packing measure for protein structure refinement and validation. Protein science. 19(10), 1991-5. Abstract  Download: sheffler10A.pdf (327.06 KB)
Sheffler, W., & Baker D. (2009).  RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation. Protein science. 18(1), 229-39. Abstract  Download: sheffler09A.pdf (503.42 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)
Meiler, J., & Baker D. (2006).  ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins. 65(3), 538-48. Abstract  Download: meiler06A.pdf (760.02 KB)
S
Kim, D. E., Blum B., Bradley P., & Baker D. (2009).  Sampling bottlenecks in de novo protein structure prediction. Journal of molecular biology. 393(1), 249-60. Abstract  Download: kim09A.pdf (1.12 MB)
Watters, A. L., & Baker D. (2004).  Searching for folded proteins in vitro and in silico. European journal of biochemistry. 271(9), 1615-22. Abstract  Download: watters04A.pdf (222.12 KB)
Kim, D. E., Gu H., & Baker D. (1998).  The sequences of small proteins are not extensively optimized for rapid folding by natural selection. Proceedings of the National Academy of Sciences of the United States of America. 95(9), 4982-6. Abstract  Download: kim98A.pdf (220.84 KB)
Kortemme, T., & Baker D. (2002).  A simple physical model for binding energy hot spots in protein-protein complexes. Proceedings of the National Academy of Sciences of the United States of America. 99(22), 14116-21. Abstract  Download: kortemme02A.pdf (200.71 KB)
Havranek, J. J., Duarte C. M., & Baker D. (2004).  A simple physical model for the prediction and design of protein-DNA interactions. Journal of molecular biology. 344(1), 59-70. Abstract  Download: havranek04A.pdf (445.63 KB)
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)
Plaxco, K. W., Riddle D. S., Grantcharova V., & Baker D. (1998).  Simplified proteins: minimalist solutions to the 'protein folding problem'.. Current opinion in structural biology. 8(1), 80-5. Abstract
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)
Kim, D. E., Yi Q., Gladwin S. T., Goldberg J. M., & Baker D. (1998).  The single helix in protein L is largely disrupted at the rate-limiting step in folding. Journal of molecular biology. 284(3), 807-15. Abstract  Download: kim98A.pdf (1.11 MB)
O'Neill, J. W., Kim D. E., Johnsen K., Baker D., & Zhang K. Y. (2001).  Single-site mutations induce 3D domain swapping in the B1 domain of protein L from Peptostreptococcus magnus. Structure. 9(11), 1017-27. Abstract  Download: o'neill01A.pdf (627.3 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)
Ruohola-Baker, H., Grell E., Chou T. B., Baker D., Jan L. Y., & Jan Y. N. (1993).  Spatially localized rhomboid is required for establishment of the dorsal-ventral axis in Drosophila oogenesis. Cell. 73(5), 953-65. Abstract  Download: ruohola-baker93A.pdf (18.04 MB)
Kuhn, M., Meiler J., & Baker D. (2004).  Strand-loop-strand motifs: prediction of hairpins and diverging turns in proteins. Proteins. 54(2), 282-8. Abstract  Download: kuhn04A.pdf (219.88 KB)
Wang, L., Althoff E. A., Bolduc J., Jiang L., Moody J., Lassila J. K., et al. (2012).  Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design. Journal of molecular biology. 415(3), 615-25. Abstract  Download: wang12A.pdf (1.22 MB)
Yi, Q., Rajagopal P., Klevit R. E., & Baker D. (2003).  Structural and kinetic characterization of the simplified SH3 domain FP1. Protein science. 12(4), 776-83. Abstract  Download: yi03A.pdf (399.69 KB)
Yarov-Yarovoy, V., DeCaen P. G., Westenbroek R. E., Pan C. - Y., Scheuer T., Baker D., et al. (2012).  Structural basis for gating charge movement in the voltage sensor of a sodium channel. Proceedings of the National Academy of Sciences of the United States of America. 109(2), E93-102. Abstract  Download: yarov-yarovoy12A.pdf (2.46 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)
Fan, E., Baker D., Fields S., Gelb M. H., Buckner F. S., Van Voorhis W. C., et al. (2008).  Structural genomics of pathogenic protozoa: an overview. Methods in molecular biology. 426, 497-513. Abstract
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)
Scalley, M. L., Nauli S., Gladwin S. T., & Baker D. (1999).  Structural transitions in the protein L denatured state ensemble. Biochemistry. 38(48), 15927-35. Abstract  Download: scalley99A.pdf (274.37 KB)
Sampathkumar, P., Lu F., Zhao X., Li Z., Gilmore J., Bain K., et al. (2010).  Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 A resolution. Proteins. 78(14), 3056-62. Download: sampathkumar10A.pdf (2.78 MB)
Zhu, J., Luo B. - H., Barth P., Schonbrun J., Baker D., & Springer T. A. (2009).  The structure of a receptor with two associating transmembrane domains on the cell surface: integrin alphaIIbbeta3. Molecular cell. 34(2), 234-49. Abstract  Download: zhu09A.pdf (4.15 MB)
Wojdyla, J. A., Fleishman S. J., Baker D., & Kleanthous C. (2012).  Structure of the Ultra-High-Affinity Colicin E2 DNase-Im2 Complex. Journal of molecular biology. Abstract  Download: wojdyla12A.pdf (2.09 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)
Raman, S., Vernon R., Thompson J., Tyka M., Sadreyev R., Pei J., et al. (2009).  Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins. 77 Suppl 9, 89-99. Abstract  Download: raman09A.pdf (500.47 KB)
Sadreyev, R. I., Shi S. Y., Baker D., & Grishin N. V. (2009).  Structure similarity measure with penalty for close non-equivalent residues. Bioinformatics. 25(10), 1259-63. Abstract  Download: sadreyev09A.pdf (259.16 KB)
Goobes, G., Goobes R., Shaw W. J., Gibson J. M., Long J. R., Raghunathan V., et al. (2008).  The structure, dynamics, and energetics of protein adsorption-lessons learned from adsorption of statherin to hydroxyapatite. Magnetic resonance in chemistry. 45(S1), S32-S47. Abstract  Download: goobes08A.pdf (523.71 KB)
Sievers, S. A., Karanicolas J., Chang H. W., Zhao A., Jiang L., Zirafi O., et al. (2011).  Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation. Nature. Abstract  Download: sievers11A.pdf (925.12 KB)
O'Neill, J. W., Kim D. E., Baker D., & Zhang K. Y. (2001).  Structures of the B1 domain of protein L from Peptostreptococcus magnus with a tyrosine to tryptophan substitution.. Acta crystallographica. Section D, Biological crystallography. 57(Pt 4), 480-7. Abstract
Malmström, L., Riffle M., Strauss C. E. M., Chivian D., Davis T. N., Bonneau R., et al. (2007).  Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS biology. 5(4), e76. Abstract  Download: malmström07A.pdf (592.42 KB)
Baker, D. (2000).  A surprising simplicity to protein folding. Nature. 405(6782), 39-42. Abstract  Download: baker00A.pdf (853.11 KB)
McFarland, B. J., Kortemme T., Yu S. F., Baker D., & Strong R. K. (2003).  Symmetry recognizing asymmetry: analysis of the interactions between the C-type lectin-like immunoreceptor NKG2D and MHC class I-like ligands. Structure. 11(4), 411-22. Abstract  Download: mcfarland03A.pdf (2.83 MB)
Windbichler, N., Menichelli M., Papathanos P. A., Thyme S. B., Li H., Ulge U. Y., et al. (2011).  A synthetic homing endonuclease-based gene drive system in the human malaria mosquito. Nature. 473(7346), 212-5. Abstract  Download: windbichler11A.pdf (563.32 KB)
T
Han, K. F., Bystroff C., & Baker D. (1997).  Three-dimensional structures and contexts associated with recurrent amino acid sequence patterns. Protein science. 6(7), 1587-90. Abstract  Download: han97A.pdf (2.35 MB)
Plaxco, K. W., Simons K. T., Ruczinski I., & Baker D. (2000).  Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics. Biochemistry. 39(37), 11177-83. Abstract  Download: plaxco00b.pdf (70.47 KB)
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)
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)
U
Krantz, B. A., Srivastava A. K., Nauli S., Baker D., Sauer R. T., & Sosnick T. R. (2002).  Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects. Nature structural biology. 9(6), 458-63. Abstract  Download: krantz02A.pdf (2.41 MB)
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)
V
Wojtowicz, W. M., Wu W., Andre I., Qian B., Baker D., & Zipursky L. S. (2007).  A vast repertoire of Dscam binding specificities arises from modular interactions of variable Ig domains. Cell. 130(6), 1134-45. Abstract  Download: wojtowicz07A.pdf (1.89 MB)
Yarov-Yarovoy, V., Baker D., & Catterall W. A. (2006).  Voltage sensor conformations in the open and closed states in ROSETTA structural models of K(+) channels. Proceedings of the National Academy of Sciences of the United States of America. 103(19), 7292-7. Abstract  Download: yarov-yarovoy06A.pdf (3.13 MB)