Publications

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1988
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)
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)
1990
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)
1991
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)
1992
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., 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)
1993
D, B., HS C., & KA D. (1993).  Coordinate-Space Formulation of Polymer Lattice Cluster Theory. Journal of Chemical Physics .  Download: baker93B.pdf (960.07 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)
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)
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)
1995
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)
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)
1996
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)
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)
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)
1997
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)
Yi, Q., Scalley M. L., Simons K. T., Gladwin S. T., & Baker D. (1997).  Characterization of the free energy spectrum of peptostreptococcal protein L. Folding & design. 2(5), 271-80. Abstract  Download: yi97A.pdf (188.99 KB)
Simons, K. T., Kooperberg C., Huang E., & Baker D. (1997).  Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. Journal of molecular biology. 268(1), 209-25. Abstract  Download: simons97A.pdf (769.01 KB)
Gu, H., Kim D. E., & Baker D. (1997).  Contrasting roles for symmetrically disposed beta-turns in the folding of a small protein. Journal of molecular biology. 274(4), 588-96. Abstract  Download: gu97A.pdf (654.1 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)
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)
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)
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
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)
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)
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)
1998
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)
Plaxco, K. W., Simons K. T., & Baker D. (1998).  Contact order, transition state placement and the refolding rates of single domain proteins. Journal of molecular biology. 277(4), 985-94. Abstract  Download: plaxco98B.pdf (304.37 KB)
Rank, J. A., & Baker D. (1998).  Contributions of solvent-solvent hydrogen bonding and van der Waals interactions to the attraction between methane molecules in water. Biophysical chemistry. 71(2-3), 199-204. Abstract  Download: rank98A.pdf (120.64 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)
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)
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)
Baker, D. (1998).  Metastable states and folding free energy barriers.. Nature structural biology. 5(12), 1021-4.
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)
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
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)
Shortle, D., Simons K. T., & Baker D. (1998).  Clustering of low-energy conformations near the native structures of small proteins. Proceedings of the National Academy of Sciences of the United States of America. 95(19), 11158-62. Abstract  Download: shortle98A.pdf (243.13 KB)
1999
Simons, K. T., Bonneau R., Ruczinski I., & Baker D. (1999).  Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins. Suppl 3, 171-6. Abstract
Alm, E., & Baker D. (1999).  Matching theory and experiment in protein folding.. Current opinion in structural biology. 9(2), 189-96. Abstract
Baker, D., & DeGrado W. F. (1999).  Engineering and design. Current opinion in structural biology. 9(4), 485-6.
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)
Gu, H., Doshi N., Kim D. E., Simons K. T., Santiago J. V., Nauli S., et al. (1999).  Robustness of protein folding kinetics to surface hydrophobic substitutions. Protein science. 8(12), 2734-41. Abstract  Download: gu99A.pdf (368.14 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)
Plaxco, K. W., Millett I. S., Segel D. J., Doniach S., & Baker D. (1999).  Chain collapse can occur concomitantly with the rate-limiting step in protein folding. Nature structural biology. 6(6), 554-6. Abstract  Download: plaxco99A.pdf (474.01 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)
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)
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)
2000
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)
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)
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)
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)
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
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)
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)
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)
Kim, D. E., Fisher C., & Baker D. (2000).  A breakdown of symmetry in the folding transition state of protein L. Journal of molecular biology. 298(5), 971-84. Abstract  Download: kim00A.pdf (416.01 KB)
Baker, D. (2000).  A surprising simplicity to protein folding. Nature. 405(6782), 39-42. Abstract  Download: baker00A.pdf (853.11 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)
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)
2001
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., 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)
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
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)
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
Lee, M. R., Baker D., & Kollman P. A. (2001).  2.1 and 1.8 A average C(alpha) RMSD structure predictions on two small proteins, HP-36 and s15. Journal of the American Chemical Society. 123(6), 1040-6. Abstract  Download: lee01A.pdf (180.46 KB)
Grantcharova, V. P., & Baker D. (2001).  Circularization changes the folding transition state of the src SH3 domain. Journal of molecular biology. 306(3), 555-63. Abstract  Download: grantcharova01A.pdf (341.23 KB)
Minard, P., Scalley-Kim M., Watters A., & Baker D. (2001).  A "loop entropy reduction" phage-display selection for folded amino acid sequences. Protein science. 10(1), 129-34. Abstract  Download: minard01A.pdf (229.21 KB)
Nauli, S., Kuhlman B., & Baker D. (2001).  Computer-based redesign of a protein folding pathway.. Nature structural biology. 8(7), 602-5. Abstract  Download: nauli01A.pdf (1.39 MB)
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)
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)
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)
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)
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)
Baker, D., & Sali A. (2001).  Protein structure prediction and structural genomics.. Science (New York, N.Y.). 294(5540), 93-6. Abstract
Kuhlman, B., O'Neill J. W., Kim D. E., Zhang K. Y., & Baker D. (2001).  Conversion of monomeric protein L to an obligate dimer by computational protein design. Proceedings of the National Academy of Sciences of the United States of America. 98(19), 10687-91. Abstract  Download: kuhlman01A.pdf (558.98 KB)
2002
Schlosshauer, M., & Baker D. (2002).  Ageneral expressionforbimolecularassociationrates withorientational constraints. Physical Chemistry B.  Download: schlosshauer02A.pdf (250.05 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)
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)
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)