Publications

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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)
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)
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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)
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)
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)
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)
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)
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)
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)
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)
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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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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Ulge, U. Y., Baker D. A., & Monnat R. J. (2011).  Comprehensive computational design of mCreI homing endonuclease cleavage specificity for genome engineering. Nucleic acids research. Abstract  Download: ulge11A.pdf (638.72 KB)
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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
Tyka, M. D., Keedy D. A., André I., DiMaio F., Song Y., Richardson D. C., et al. (2010).  Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping. Journal of molecular biology. Abstract  Download: tyka10A.pdf (2.13 MB)
Tsemekhman, K., Goldschmidt L., Eisenberg D., & Baker D. (2007).  Cooperative hydrogen bonding in amyloid formation. Protein science. 16(4), 761-4. Abstract  Download: tsemekhman07A.pdf (260.96 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)
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)
Tress, M., Cheng J., Baldi P., Joo K., Lee J., Seo J. - H., et al. (2007).  Assessment of predictions submitted for the CASP7 domain prediction category. Proteins. 69 Suppl 8, 137-51. Abstract  Download: tress07A.pdf (1.5 MB)
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
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)
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)
Thompson, M. J., Sievers S. A., Karanicolas J., Ivanova M. I., Baker D., & Eisenberg D. (2006).  The 3D profile method for identifying fibril-forming segments of proteins. Proceedings of the National Academy of Sciences of the United States of America. 103(11), 4074-8. Abstract  Download: thompson06A.pdf (738.97 KB)
Thompson, J. M., Sgourakis N. G., Liu G., Rossi P., Tang Y., Mills J. L., et al. (2012).  Accurate protein structure modeling using sparse NMR data and homologous structure information.. Proceedings of the National Academy of Sciences of the United States of America. 109(25), 9875-80. 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)
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
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)
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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
Svensson, H. G., Wedemeyer W. J., Ekstrom J. L., Callender D. R., Kortemme T., Kim D. E., et al. (2004).  Contributions of amino acid side chains to the kinetics and thermodynamics of the bivalent binding of protein L to Ig kappa light chain. Biochemistry. 43(9), 2445-57. Abstract  Download: svensson04A.pdf (522.01 KB)
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)
Spreter, T., Yip C. K., Sanowar S., André I., Kimbrough T. G., Vuckovic M., et al. (2009).  A conserved structural motif mediates formation of the periplasmic rings in the type III secretion system. Nature structural & molecular biology. 16(5), 468-76. Abstract  Download: spreter09A.pdf (2.37 MB)
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)
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)
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)
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)
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
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)
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)
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)
Siegel, J. B., Zanghellini A., Lovick H. M., Kiss G., Lambert A. R., St Clair J. L., et al. (2010).  Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science. 329(5989), 309-13. Abstract  Download: siegel10A.pdf (1.55 MB)
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)
Shen, Y., Lange O., Delaglio F., Rossi P., Aramini J. M., Liu G., et al. (2008).  Consistent blind protein structure generation from NMR chemical shift data. Proceedings of the National Academy of Sciences of the United States of America. 105(12), 4685-90. Abstract  Download: shen08A.pdf (1.01 MB)
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)
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)
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)
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)
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)
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)
Schueler-Furman, O., & Baker D. (2003).  Conserved residue clustering and protein structure prediction. Proteins. 52(2), 225-35. Abstract  Download: schueler-furman03A.pdf (245.13 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)
Schonbrun, J., Wedemeyer W. J., & Baker D. (2002).  Protein structure prediction in 2002.. Current opinion in structural biology. 12(3), 348-54. Abstract
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)
Schlosshauer, M., & Baker D. (2002).  Ageneral expressionforbimolecularassociationrates withorientational constraints. Physical Chemistry B.  Download: schlosshauer02A.pdf (250.05 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)
Scalley-Kim, M., & Baker D. (2004).  Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection. Journal of molecular biology. 338(3), 573-83. Abstract  Download: scalley-kim04A.pdf (537.27 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)
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)
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)
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
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)
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)
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)
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)
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)
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)
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)
S, R., B Q., D B., & RC W. (2008).  Advances in Rosetta Protein Structure Prediction on Massively Parallel Systems. Journal of Research and Development . 52(1-2):7-17, Abstract  Download: raman08A.pdf (446.3 KB)