Publications

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Journal Article
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)
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)
Grantcharova, V. P., Riddle D. S., & Baker D. (2000).  Long-range order in the src SH3 folding transition state. Proceedings of the National Academy of Sciences of the United States of America. 97(13), 7084-9. Abstract  Download: grantcharova00A.pdf (313 KB)
Scalley-Kim, M., Minard P., & Baker D. (2003).  Low free energy cost of very long loop insertions in proteins. Protein science. 12(2), 197-206. Abstract  Download: scalley-kim03A.pdf (131.71 KB)
Das, R., & Baker D. (2008).  Macromolecular modeling with rosetta. Annual review of biochemistry. 77, 363-82. Abstract  Download: das08A.pdf (1.13 MB)
Alm, E., & Baker D. (1999).  Matching theory and experiment in protein folding.. Current opinion in structural biology. 9(2), 189-96. Abstract
Grantcharova, V., Alm E. J., Baker D., & Horwich A. L. (2001).  Mechanisms of protein folding.. Current opinion in structural biology. 11(1), 70-82. Abstract
Baker, D. (1998).  Metastable states and folding free energy barriers.. Nature structural biology. 5(12), 1021-4.
Szeto, M. D., Boissel S. J. S., Baker D., & Thyme S. B. (2011).  Mining endonuclease cleavage determinants in genomic sequence data.. The Journal of biological chemistry. 286(37), 32617-27. Abstract
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)
Lacy, B. D., Lin H. C., Melnyk R. A., Schueler-Furman O., Reither L., Cunningham K., et al. (2005).  A model of anthrax toxin lethal factor bound to protective antigen. Proceedings of the National Academy of Sciences of the United States of America. 102(45), 16409-14. Abstract  Download: lacy05A.pdf (621.23 KB)
Rohl, C. A., Strauss C. E. M., Chivian D., & Baker D. (2004).  Modeling structurally variable regions in homologous proteins with rosetta. Proteins. 55(3), 656-77. Abstract  Download: rohl04A.pdf (425.56 KB)
Lee, M. R., Tsai J., Baker D., & Kollman P. A. (2001).  Molecular dynamics in the endgame of protein structure prediction. Journal of molecular biology. 313(2), 417-30. Abstract  Download: lee01B.pdf (814.49 KB)
Havranek, J. J., & Baker D. (2009).  Motif-directed flexible backbone design of functional interactions. Protein science. 18(6), 1293-305. Abstract  Download: havranek09A.pdf (753.33 KB)
Yarov-Yarovoy, V., Schonbrun J., & Baker D. (2006).  Multipass membrane protein structure prediction using Rosetta. Proteins. 62(4), 1010-25. Abstract  Download: yarov-yarovoy06B.pdf (1.31 MB)
Lengyel, C. S. E., Willis L. J., Mann P., Baker D., Kortemme T., Strong R. K., et al. (2007).  Mutations designed to destabilize the receptor-bound conformation increase MICA-NKG2D association rate and affinity. The Journal of biological chemistry. 282(42), 30658-66. Abstract  Download: lengyel07A.pdf (454.13 KB)
Kuhlman, B., & Baker D. (2000).  Native protein sequences are close to optimal for their structures. Proceedings of the National Academy of Sciences of the United States of America. 97(19), 10383-8. Abstract  Download: kuhlman00A.pdf (142.94 KB)
Zanghellini, A., Jiang L., Wollacott A. M., Cheng G., Meiler J., Althoff E. A., et al. (2006).  New algorithms and an in silico benchmark for computational enzyme design. Protein science : a publication of the Protein Society. 15(12), 2785-94. Abstract  Download: zanghellini06A.pdf (497.12 KB)
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)
McBeth, C., Seamons A., Pizarro J. C., Fleishman S. J., Baker D., Kortemme T., et al. (2008).  A new twist in TCR diversity revealed by a forbidden alphabeta TCR. Journal of molecular biology. 375(5), 1306-19. Abstract  Download: mcbeth08A.pdf (5.02 MB)
Yi, Q., Scalley-Kim M. L., Alm E. J., & Baker D. (2000).  NMR characterization of residual structure in the denatured state of protein L. Journal of molecular biology. 299(5), 1341-51. Abstract  Download: yia00A.pdf (309.07 KB)
Raman, S., Lange O. F., Rossi P., Tyka M., Wang X., Aramini J., et al. (2010).  NMR structure determination for larger proteins using backbone-only data. Science. 327(5968), 1014-8. Abstract  Download: raman10A.pdf (2.02 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)
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)
Whitehead, T. A., Chevalier A., Song Y., Dreyfus C., Fleishman S. J., De Mattos C., et al. (2012).  Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing. Nature biotechnology. Abstract  Download: whitehead12A.pdf (1.38 MB)
Khersonsky, O., Röthlisberger D., Wollacott A. M., Murphy P., Dym O., Albeck S., et al. (2011).  Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution. Journal of molecular biology. 407(3), 391-412. Abstract  Download: khersonsky11A.pdf (1.77 MB)
Kortemme, T., Morozov A. V., & Baker D. (2003).  An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. Journal of molecular biology. 326(4), 1239-59. Abstract  Download: kortemmea03A.pdf (2.13 MB)
Nivón, L. G., Moretti R., & Baker D. (2013).  A Pareto-optimal refinement method for protein design scaffolds.. PloS one. 8(4), e59004. Abstract
Gu, H., Yi Q., Bray S. T., Riddle D. S., Shiau A. K., & Baker D. (1995).  A phage display system for studying the sequence determinants of protein folding. Protein science. 4(6), 1108-17. Abstract  Download: gu95A.pdf (4.61 MB)
Terwilliger, T. C., DiMaio F., Read R. J., Baker D., Bunkóczi G., Adams P. D., et al. (2012).  phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta.. Journal of structural and functional genomics. 13(2), 81-90. Abstract
Misura, K. M. S., Chivian D., Rohl C. A., Kim D. E., & Baker D. (2006).  Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proceedings of the National Academy of Sciences of the United States of America. 103(14), 5361-6. Abstract  Download: misura06A.pdf (2.12 MB)
Kim, K. M., Yi E. C., Baker D., & Zhang K. Y. (2001).  Post-translational modification of the N-terminal His tag interferes with the crystallization of the wild-type and mutant SH3 domains from chicken src tyrosine kinase. Acta crystallographica. Section D. 57(Pt 5), 759-62. Abstract  Download: kim01A.pdf (274.8 KB)
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)
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)
Yi, Q., Bystroff C., Rajagopal P., Klevit R. E., & Baker D. (1998).  Prediction and structural characterization of an independently folding substructure in the src SH3 domain. Journal of molecular biology. 283(1), 293-300. Abstract  Download: yi98A.pdf (785.68 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)
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)
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)
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)
Wollacott, A. M., Zanghellini A., Murphy P., & Baker D. (2007).  Prediction of structures of multidomain proteins from structures of the individual domains. Protein science. 16(2), 165-75. Abstract  Download: wollacott07A.pdf (1.04 MB)
Wang, C., Vernon R., Lange O., Tyka M., & Baker D. (2010).  Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry. Protein science. 19(3), 494-506. Abstract  Download: wang10A.pdf (571.91 KB)
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)
Koga, N., Tatsumi-Koga R., Liu G., Xiao R., Acton T. B., Montelione G. T., et al. (2012).  Principles for designing ideal protein structures.. Nature. 491(7423), 222-7. Abstract  Download: nature11600.pdf (2.17 MB)
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)
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)
Sadreyev, R. I., Baker D., & Grishin N. V. (2003).  Profile-profile comparisons by COMPASS predict intricate homologies between protein families. Protein science. 12(10), 2262-72. Abstract  Download: sadreyev03A.pdf (1.02 MB)
Misura, K. M. S., & Baker D. (2005).  Progress and challenges in high-resolution refinement of protein structure models. Proteins. 59(1), 15-29. Abstract  Download: misura05A.pdf (651.28 KB)
Schueler-Furman, O., Wang C., Bradley P., Misura K., & Baker D. (2005).  Progress in modeling of protein structures and interactions. Science. 310(5748), 638-42. Abstract  Download: schueler-furman05B.pdf (313.68 KB)
Schueler-Furman, O., Wang C., & Baker D. (2005).  Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins. 60(2), 187-94. Abstract  Download: schueler-rurman05A.pdf (333.32 KB)
Simons, K. T., Strauss C., & Baker D. (2001).  Prospects for ab initio protein structural genomics. Journal of molecular biology. 306(5), 1191-9. Abstract  Download: simons01A.pdf (282.77 KB)
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)
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
Scalley, M. L., & Baker D. (1997).  Protein folding kinetics exhibit an Arrhenius temperature dependence when corrected for the temperature dependence of protein stability. Proceedings of the National Academy of Sciences of the United States of America. 94(20), 10636-40. Abstract  Download: scalley97A.pdf (249.15 KB)
Schmitz, C., Vernon R., Otting G., Baker D., & Huber T. (2012).  Protein Structure Determination from Pseudocontact Shifts Using ROSETTA. Journal of molecular biology. Abstract  Download: schmitz12A.pdf (1.03 MB)
Kim, D. E., Chivian D., & Baker D. (2004).  Protein structure prediction and analysis using the Robetta server. Nucleic acids research. 32(Web Server issue), W526-31. Abstract  Download: kim04A.pdf (890.15 KB)
Baker, D., & Sali A. (2001).  Protein structure prediction and structural genomics.. Science (New York, N.Y.). 294(5540), 93-6. Abstract
Schonbrun, J., Wedemeyer W. J., & Baker D. (2002).  Protein structure prediction in 2002.. Current opinion in structural biology. 12(3), 348-54. Abstract
Rohl, C. A., Strauss C. E. M., Misura K. M. S., & Baker D. (2004).  Protein structure prediction using Rosetta.. Methods in enzymology. 383, 66-93.
Payne, G. S., Baker D., van Tuinen E., & Schekman R. (1988).  Protein transport to the vacuole and receptor-mediated endocytosis by clathrin heavy chain-deficient yeast. The Journal of cell biology. 106(5), 1453-61. Abstract  Download: payne88A.pdf (2.11 MB)
Morozov, A. V., Havranek J. J., Baker D., & Siggia E. D. (2005).  Protein-DNA binding specificity predictions with structural models. Nucleic acids research. 33(18), 5781-98. Abstract  Download: morozov05A.pdf (293.94 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)
Gray, J. J., Moughon S. E., Kortemme T., Schueler-Furman O., Misura K. M. S., Morozov A. V., et al. (2003).  Protein-protein docking predictions for the CAPRI experiment. Proteins. 52(1), 118-22. Abstract  Download: gray03B.pdf (467.92 KB)
Wang, C., Bradley P., & Baker D. (2007).  Protein-protein docking with backbone flexibility. Journal of molecular biology. 373(2), 503-19. Abstract  Download: wang07A.pdf (1.57 MB)
Gray, J. J., Moughon S., Wang C., Schueler-Furman O., Kuhlman B., Rohl C. A., et al. (2003).  Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. Journal of molecular biology. 331(1), 281-99. Abstract  Download: gray03A.pdf (2.12 MB)
Weerapana, E., Wang C., Simon G. M., Richter F., Khare S., Dillon M. B. D., et al. (2010).  Quantitative reactivity profiling predicts functional cysteines in proteomes. Nature. 468(7325), 790-5. Abstract  Download: weerapana10A.pdf (608.01 KB)
Qiu, J., Sheffler W., Baker D., & Noble W. S. (2008).  Ranking predicted protein structures with support vector regression. Proteins. 71(3), 1175-82. Abstract  Download: qiu08A.pdf (320.82 KB)
Meiler, J., & Baker D. (2003).  Rapid protein fold determination using unassigned NMR data. Proceedings of the National Academy of Sciences of the United States of America. 100(26), 15404-9. Abstract  Download: meiler03B.pdf (593 KB)
Song, G., Lazar G. A., Kortemme T., Shimaoka M., Desjarlais J. R., Baker D., et al. (2006).  Rational design of intercellular adhesion molecule-1 (ICAM-1) variants for antagonizing integrin lymphocyte function-associated antigen-1-dependent adhesion. The Journal of biological chemistry. 281(8), 5042-9. Abstract  Download: song06A.pdf (277.35 KB)
Jardine, J., Julien J. - P., Menis S., Ota T., Kalyuzhniy O., McGuire A., et al. (2013).  Rational HIV immunogen design to target specific germline B cell receptors.. Science (New York, N.Y.). 340(6133), 711-6. Abstract
Luo, B. - H., Karanicolas J., Harmacek L. D., Baker D., & Springer T. A. (2009).  Rationally designed integrin beta3 mutants stabilized in the high affinity conformation. The Journal of biological chemistry. 284(6), 3917-24. Abstract  Download: luo09A.pdf (673.21 KB)
Schlosshauer, M., & Baker D. (2004).  Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness. Protein science. 13(6), 1660-9. Abstract  Download: schlosshauer04A.pdf (185.7 KB)
Sood, V. D., & Baker D. (2006).  Recapitulation and design of protein binding peptide structures and sequences. Journal of molecular biology. 357(3), 917-27. Abstract  Download: sood06A.pdf (497.29 KB)
Saunders, C. T., & Baker D. (2005).  Recapitulation of protein family divergence using flexible backbone protein design. Journal of molecular biology. 346(2), 631-44. Abstract  Download: saundersa05A.pdf (639.35 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)
Han, K. F., & Baker D. (1995).  Recurring local sequence motifs in proteins. Journal of molecular biology. 251(1), 176-87. Abstract  Download: han95A.pdf (297.22 KB)
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
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)
Stankunas, K., Bayle H. J., Havranek J. J., Wandless T. J., Baker D., Crabtree G. R., et al. (2007).  Rescue of degradation-prone mutants of the FK506-rapamycin binding (FRB) protein with chemical ligands. Chembiochem : a European journal of chemical biology. 8(10), 1162-9. Abstract  Download: stankunas07A.pdf (579.3 KB)
Larson, S. M., Ruczinski I., Davidson A. R., Baker D., & Plaxco K. W. (2002).  Residues participating in the protein folding nucleus do not exhibit preferential evolutionary conservation. Journal of molecular biology. 316(2), 225-33. Abstract  Download: larson02A.pdf (213.29 KB)