Publications

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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)
Sprague, E. R., Wang C., Baker D., & Bjorkman P. J. (2006).  Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging. PLoS biology. 4(6), e148. Abstract  Download: sprague06A.pdf (539.35 KB)
Li, M., DiMaio F., Zhou D., Gustchina A., Lubkowski J., Dauter Z., et al. (2011).  Crystal structure of XMRV protease differs from the structures of other retropepsins. Nature structural & molecular biology. 18(2), 227-9. Abstract  Download: li11A.pdf (663.49 KB)
Nauli, S., Kuhlman B., Le Trong I., Stenkamp R. E., Teller D., & Baker D. (2002).  Crystal structures and increased stabilization of the protein G variants with switched folding pathways NuG1 and NuG2. Protein science. 11(12), 2924-31. Abstract  Download: nauli02A.pdf (257.77 KB)
Johnsen, K., O'Neill J. W., Kim D. E., Baker D., & Zhang K. Y. (2000).  Crystallization and preliminary X-ray diffraction studies of mutants of B1 IgG-binding domain of protein L from Peptostreptococcus magnus. Acta crystallographica. Section D. 56(Pt 4), 506-8. Abstract  Download: johnsen00A.pdf (244.36 KB)
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Jiang, L., Althoff E. A., Clemente F. R., Doyle L., Röthlisberger D., Zanghellini A., et al. (2008).  De novo computational design of retro-aldol enzymes. Science. 319(5868), 1387-91. Abstract  Download: jiang08A.pdf (629.34 KB)
Rohl, C. A., & Baker D. (2002).  De novo determination of protein backbone structure from residual dipolar couplings using Rosetta. Journal of the American Chemical Society. 124(11), 2723-9. Abstract  Download: rohl02A.pdf (265.13 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)
Karanicolas, J., Corn J. E., Chen I., Joachimiak L. A., Dym O., Peck S. H., et al. (2011).  A De Novo Protein Binding Pair By Computational Design and Directed Evolution. Molecular cell. Abstract  Download: karanicolas11A.pdf (1.2 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
Shen, Y., Vernon R., Baker D., & Bax A. (2009).  De novo protein structure generation from incomplete chemical shift assignments. Journal of biomolecular NMR. 43(2), 63-78. Abstract  Download: shen09A.pdf (2.53 MB)
Kuhlman, B., Dantas G., Ireton G. C., Varani G., Stoddard B. L., & Baker D. (2003).  Design of a novel globular protein fold with atomic-level accuracy. Science. 302(5649), 1364-8. Abstract  Download: kuhlman03A.pdf (2.79 MB)
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)
Rank, J. A., & Baker D. (1997).  A desolvation barrier to hydrophobic cluster formation may contribute to the rate-limiting step in protein folding. Protein science. 6(2), 347-54. Abstract  Download: rank97A.pdf (1.76 MB)
Thayer, E. C., Bystroff C., & Baker D. (2000).  Detection of protein coding sequences using a mixture model for local protein amino acid sequence. Journal of computational biology : a journal of computational molecular cell biology. 7(1-2), 317-27. Abstract  Download: thayer00A.pdf (244.63 KB)
Lange, O. F., Rossi P., Sgourakis N. G., Song Y., Lee H. - W., Aramini J. M., et al. (2012).  Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples.. Proceedings of the National Academy of Sciences of the United States of America. 109(27), 10873-8. Abstract
Sgourakis, N. G., Lange O. F., DiMaio F., André I., Fitzkee N. C., Rossi P., et al. (2011).  Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings. Journal of the American Chemical Society. Abstract  Download: sgourakis11A.pdf (655.81 KB)
Yi, Q., & Baker D. (1996).  Direct evidence for a two-state protein unfolding transition from hydrogen-deuterium exchange, mass spectrometry, and NMR. Protein science. 5(6), 1060-6. Abstract  Download: yi96A.pdf (4.65 MB)
Shcherbata, H. R., Yatsenko A. S., Patterson L., Sood V. D., Nudel U., Yaffe D., et al. (2007).  Dissecting muscle and neuronal disorders in a Drosophila model of muscular dystrophy. The EMBO journal. 26(2), 481-93. Abstract  Download: shcherbata07A.pdf (916.91 KB)
Ruczinski, I., Kooperberg C., Bonneau R., & Baker D. (2002).  Distributions of beta sheets in proteins with application to structure prediction. Proteins. 48(1), 85-97. Abstract  Download: ruczinski02A.pdf (1017.65 KB)
Sawaya, M. R., Wojtowicz W. M., Andre I., Qian B., Wu W., Baker D., et al. (2008).  A double S shape provides the structural basis for the extraordinary binding specificity of Dscam isoforms. Cell. 134(6), 1007-18. Abstract  Download: sawaya08A.pdf (6.42 MB)
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Millet, O., Mittermaier A., Baker D., & Kay L. E. (2003).  The effects of mutations on motions of side-chains in protein L studied by 2H NMR dynamics and scalar couplings. Journal of molecular biology. 329(3), 551-63. Abstract  Download: millet03A.pdf (1.03 MB)
Wedemeyer, W. J., & Baker D. (2003).  Efficient minimization of angle-dependent potentials for polypeptides in internal coordinates. Proteins. 53(2), 262-72. Abstract  Download: wedemeyer03A.pdf (363.38 KB)
Tyka, M. D., Jung K., & Baker D. (2012).  Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers.. Journal of computational chemistry. 33(31), 2483-91. Abstract
Morozov, A. V., Tsemekhman K., & Baker D. (2006).  Electron density redistribution accounts for half the cooperativity of alpha helix formation. The journal of physical chemistry. B. 110(10), 4503-5. Abstract  Download: morozov06A.pdf (132.16 KB)
Ofek, G., Guenaga J. F., Schief W. R., Skinner J., Baker D., Wyatt R., et al. (2010).  Elicitation of structure-specific antibodies by epitope scaffolds. Proceedings of the National Academy of Sciences of the United States of America. 107(42), 17880-7. Abstract  Download: ofek10A.pdf (2.68 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)
Wargacki, A. J., Leonard E., Win M. N., Regitsky D. D., Santos C. N. S., Kim P. B., et al. (2012).  An engineered microbial platform for direct biofuel production from brown macroalgae. Science. 335(6066), 308-13. Abstract  Download: wargacki12A.pdf (1.41 MB)
Baker, D., & DeGrado W. F. (1999).  Engineering and design. Current opinion in structural biology. 9(4), 485-6.
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
Kellogg, E. H., Lange O. F., & Baker D. (2012).  Evaluation and optimization of discrete state models of protein folding.. The journal of physical chemistry. B. 116(37), 11405-13. Abstract
Kiss, G., Röthlisberger D., Baker D., & Houk K. N. (2010).  Evaluation and ranking of enzyme designs. Protein science. 19(9), 1760-73. Abstract  Download: kiss10A.pdf (884.51 KB)
Morozov, A., Kortemme T., & Baker D. (2003).  Evaluation of Models of Electrostatic Interactions in Proteins. Journal of Physical Chemistry B. 107(9), 2075-2090. Abstract  Download: morozov03A.pdf (691.51 KB)
Saunders, C. T., & Baker D. (2002).  Evaluation of structural and evolutionary contributions to deleterious mutation prediction. Journal of molecular biology. 322(4), 891-901. Abstract  Download: saunders02A.pdf (484.42 KB)
Plaxco, K. W., Larson S., Ruczinski I., Riddle D. S., Thayer E. C., Buchwitz B., et al. (2000).  Evolutionary conservation in protein folding kinetics. Journal of molecular biology. 298(2), 303-12. Abstract  Download: plaxco00a.pdf (214.04 KB)
Baker, D. (2010).  An exciting but challenging road ahead for computational enzyme design. Protein science.  Download: baker10A.pdf (58.56 KB)
Riddle, D. S., Grantcharova V. P., Santiago J. V., Alm E., Ruczinski I., & Baker D. (1999).  Experiment and theory highlight role of native state topology in SH3 folding. Nature structural biology. 6(11), 1016-24. Abstract  Download: riddle99A.pdf (951.11 KB)
Keeble, A. H., Joachimiak L. A., Maté M. J., Meenan N., Kirkpatrick N., Baker D., et al. (2008).  Experimental and computational analyses of the energetic basis for dual recognition of immunity proteins by colicin endonucleases. Journal of molecular biology. 379(4), 745-59. Abstract  Download: keeble08A.pdf (1.25 MB)
Thyme, S. B., Jarjour J., Takeuchi R., Havranek J. J., Ashworth J., Scharenberg A. M., et al. (2009).  Exploitation of binding energy for catalysis and design. Nature. 461(7268), 1300-4. Abstract  Download: thyme09A.pdf (971.19 KB)
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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)
Grantcharova, V. P., & Baker D. (1997).  Folding dynamics of the src SH3 domain. Biochemistry. 36(50), 15685-92. Abstract  Download: grantcharova97A.pdf (171.64 KB)
Goobes, G., Goobes R., Schueler-Furman O., Baker D., Stayton P. S., & Drobny G. P. (2006).  Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals. Proceedings of the National Academy of Sciences of the United States of America. 103(44), 16083-8. Abstract  Download: goobes06A.pdf (725.15 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)
Tang, Y., Schneider W. M., Shen Y., Raman S., Inouye M., Baker D., et al. (2010).  Fully automated high-quality NMR structure determination of small (2)H-enriched proteins. Journal of structural and functional genomics. 11(4), 223-32. Abstract  Download: tang10A.pdf (451.53 KB)
Meiler, J., & Baker D. (2005).  The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy. Journal of magnetic resonance. 173(2), 310-6. Abstract  Download: meiler05A.pdf (657.1 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)
Riddle, D. S., Santiago J. V., Bray-Hall S. T., Doshi N., Grantcharova V. P., Yi Q., et al. (1997).  Functional rapidly folding proteins from simplified amino acid sequences. Nature structural biology. 4(10), 805-9. Abstract  Download: riddle97A.pdf (671.68 KB)
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Han, K. F., & Baker D. (1996).  Global properties of the mapping between local amino acid sequence and local structure in proteins. Proceedings of the National Academy of Sciences of the United States of America. 93(12), 5814-8. Abstract  Download: han96A.pdf (938.22 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)
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Guenaga, J., Dosenovic P., Ofek G., Baker D., Schief W. R., Kwong P. D., et al. (2011).  Heterologous epitope-scaffold prime:boosting immuno-focuses B cell responses to the HIV-1 gp41 2F5 neutralization determinant. PloS one. 6(1), e16074. Abstract  Download: guenaga11A.pdf (1.95 MB)
Tsai, J., Levitt M., & Baker D. (1999).  Hierarchy of structure loss in MD simulations of src SH3 domain unfolding. Journal of molecular biology. 291(1), 215-25. Abstract  Download: tsai99A.pdf (666.2 KB)
Fowler, D. M., Araya C. L., Fleishman S. J., Kellogg E. H., Stephany J. J., Baker D., et al. (2010).  High-resolution mapping of protein sequence-function relationships. Nature methods. 7(9), 741-6. Abstract  Download: fowler10A.pdf (1.09 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)
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)
Qian, B., Raman S., Das R., Bradley P., McCoy A. J., Read R. J., et al. (2007).  High-resolution structure prediction and the crystallographic phase problem. Nature. 450(7167), 259-64. Abstract  Download: qian07A.pdf (1.73 MB)
Watters, A. L., Deka P., Corrent C., Callender D., Varani G., Sosnick T., et al. (2007).  The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection. Cell. 128(3), 613-24. Abstract  Download: watters07A.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)
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)
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Grantcharova, V. P., Riddle D. S., Santiago J. V., & Baker D. (1998).  Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain. Nature structural biology. 5(8), 714-20. Abstract  Download: grantcharova98A.pdf (833.81 KB)
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)
Thyme, S. B., Baker D., & Bradley P. (2012).  Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design.. Journal of molecular biology. 419(3-4), 255-74. Abstract
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)
Tsai, J., Bonneau R., Morozov A. V., Kuhlman B., Rohl C. A., & Baker D. (2003).  An improved protein decoy set for testing energy functions for protein structure prediction. Proteins. 53(1), 76-87. Abstract  Download: Tsai03A.pdf (376.65 KB)
Simons, K. T., Ruczinski I., Kooperberg C., Fox B. A., Bystroff C., & Baker D. (1999).  Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins. 34(1), 82-95. Abstract  Download: simons98A.pdf (313.04 KB)
Wang, C., Schueler-Furman O., & Baker D. (2005).  Improved side-chain modeling for protein-protein docking. Protein science. 14(5), 1328-39. Abstract  Download: wang05A.pdf (736.4 KB)
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)
Qian, B., Ortiz A. R., & Baker D. (2004).  Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. Proceedings of the National Academy of Sciences of the United States of America. 101(43), 15346-51. Abstract  Download: qian04A.pdf (573.21 KB)
Ramelot, T. A., Raman S., Kuzin A. P., Xiao R., Ma L. - C., Acton T. B., et al. (2009).  Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study. Proteins. 75(1), 147-67. Abstract  Download: ramelot09A.pdf (790.67 KB)
Krieger, E., Joo K., Lee J., Lee J., Raman S., Thompson J., et al. (2009).  Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins. 77 Suppl 9, 114-22. Abstract  Download: krieger09A.pdf (646.49 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)
Thompson, J., & Baker D. (2011).  Incorporation of evolutionary information into Rosetta comparative modeling.. Proteins. 79(8), 2380-8. Abstract  Download: thompson11A.pdf (624.44 KB)
Eiben, C. B., Siegel J. B., Bale J. B., Cooper S., Khatib F., Shen B. W., et al. (2012).  Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nature biotechnology. 30(2), 190-2. Abstract  Download: eiben12A.pdf (552.17 KB)
Sanowar, S., Singh P., Pfuetzner R. A., André I., Zheng H., Spreter T., et al. (2010).  Interactions of the Transmembrane Polymeric Rings of the Salmonella enterica Serovar Typhimurium Type III Secretion System. mBio. 1(3),  Abstract  Download: sanowar10A.pdf (1.65 MB)
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Röthlisberger, D., Khersonsky O., Wollacott A. M., Jiang L., DeChancie J., Betker J., et al. (2008).  Kemp elimination catalysts by computational enzyme design. Nature. 453(7192), 190-5. Abstract  Download: röthlisberger08A.pdf (744.82 KB)
Scalley, M. L., Yi Q., Gu H., McCormack A., Yates J. R., & Baker D. (1997).  Kinetics of folding of the IgG binding domain of peptostreptococcal protein L.. Biochemistry. 36(11), 3373-82. Abstract
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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)
Plaxco, K. W., & Baker D. (1998).  Limited internal friction in the rate-limiting step of a two-state protein folding reaction. Proceedings of the National Academy of Sciences of the United States of America. 95(23), 13591-6. Abstract  Download: plaxco98A.pdf (205 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)