Baker Lab Publications

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Baker Lab Publications

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In Press

Fleishman, S. J., Whitehead T. A., Ekiert D. C., Dreyfus C., Corn J. E., Strauch E. - M., et al. (In Press). Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science.

DiMaio, F., Terwilliger T., Read R., Wlodawar A., & D. B. (In Press). Increasing the Radius of Convergence of Molecular Replacement by Density and Energy Guided Protein Structure Optimization. Nature.

2011

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)

Kellogg, E. H., Leaver-Fay A., & Baker D. (2011). Role of conformational sampling in computing mutation-induced changes in protein structure and stability. Proteins. 79(3), 830-8. Abstract Download: kellogg11A.pdf (430.48 KB)

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)

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)

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)

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)

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)

Fleishman, S. J., Khare S. D., Koga N., & Baker D. (2011). Restricted sidechain plasticity in the structures of native proteins and complexes. Protein science. 20(4), 753-7. Abstract Download: fleishman11A.pdf (295.85 KB)

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)

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)

2010

Correia, B. E., Ban Y. - E. A., Holmes M. A., Xu H., Ellingson K., Kraft Z., et al. (2010). Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope. Structure. 18(9), 1116-26. Abstract Download: correia10A.pdf (1.12 MB)

Ashworth, J., Taylor G. K., Havranek J. J., Quadri A. S., Stoddard B. L., & Baker D. (2010). Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs. Nucleic acids research. 38(16), 5601-8. Abstract Download: ashworth10.pdf (3.02 MB)

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)

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)

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)

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)

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)

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)

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)

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)

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)

Raman, S., Huang Y. J., Mao B., Rossi P., Aramini J. M., Liu G., et al. (2010). Accurate automated protein NMR structure determination using unassigned NOESY data. Journal of the American Chemical Society. 132(1), 202-7. Abstract Download: raman10A.pdf (3.49 MB)

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)

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)

Liu, L., Murphy P., Baker D., & Lutz S. (2010). Computational design of orthogonal nucleoside kinases. Chemical communications. 46(46), 8803-5. Abstract Download: liu10A.pdf (1.22 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)

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. (2010). An exciting but challenging road ahead for computational enzyme design. Protein science. Download: baker10A.pdf (58.56 KB)

Das, R., Karanicolas J., & Baker D. (2010). Atomic accuracy in predicting and designing noncanonical RNA structure. Nature methods. 7(4), 291-4. Abstract Download: das10A.pdf (1.13 MB)

Cooper, S., Treuille A., Barbero J., Leaver-Fay A., Tuite K., Khatib F., et al. (2010). The Challenge of Designing Scientific Discovery Games. Proceedings of the Fifth international Conference on the Foundations of Digital Games. Abstract Download: cooper10A.pdf (1.19 MB)

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)

2009

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)

Davis, I. W., Raha K., Head M. S., & Baker D. (2009). Blind docking of pharmaceutically relevant compounds using RosettaLigand. Protein science. 18(9), 1998-2002. Abstract Download: davis09A.pdf (261.62 KB)

Rosato, A., Bagaria A., Baker D., Bardiaux B., Cavalli A., Doreleijers J. F., et al. (2009). CASD-NMR: critical assessment of automated structure determination by NMR. Nature methods. 6(9), 625-6. Download: rosato09A.pdf (175.47 KB)

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)

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)

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)

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)

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)

Murphy, P. M., Bolduc J. M., Gallaher J. L., Stoddard B. L., & Baker D. (2009). Alteration of enzyme specificity by computational loop remodeling and design. Proceedings of the National Academy of Sciences of the United States of America. 106(23), 9215-20. Abstract Download: murphy09A.pdf (954.03 KB)

Ashworth, J., & Baker D. (2009). Assessment of the optimization of affinity and specificity at protein-DNA interfaces. Nucleic acids research. 37(10), e73. Abstract Download: ashworth09A.pdf (3.58 MB)

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)

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)

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)

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)

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)

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)

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)

Kidd, B. A., Baker D., & Thomas W. E. (2009). Computation of conformational coupling in allosteric proteins. PLoS computational biology. 5(8), e1000484. Abstract Download: kidd09A.pdf (484.92 KB)

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)

Muratore, K. E., Seeliger M. A., Wang Z., Fomina D., Neiswinger J., Havranek J. J., et al. (2009). Comparative analysis of mutant tyrosine kinase chemical rescue. Biochemistry. 48(15), 3378-86. Abstract Download: muratore09A.pdf (318.66 KB)

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)

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)

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)

Ban, Y. A., Correia B. E., Holmes M., Boni E., Sather N., Bretz C., et al. (2009). 4e10 epitope-scaffolds mimic the antibody-bound epitope conformation and block neutralization by sera from rare HIV+ individuals. Retrovirology. 6, Download: ban09A.pdf (130.41 KB)

2008

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)

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)

Alexandrova, A. N., Röthlisberger D., Baker D., & Jorgensen W. L. (2008). Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination. Journal of the American Chemical Society. 130(47), 15907-15. Abstract Download: alexandrova08A.pdf (4.49 MB)

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)

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)

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)

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)

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)

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)

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)

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)

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)

Das, R., & Baker D. (2008). Macromolecular modeling with rosetta. Annual review of biochemistry. 77, 363-82. Abstract Download: das08A.pdf (1.13 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

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)

2007

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)

Das, R., & Baker D. (2007). Automated de novo prediction of native-like RNA tertiary structures. Proceedings of the National Academy of Sciences of the United States of America. 104(37), 14664-9. Abstract Download: das07A.pdf (1.29 MB)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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., 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)

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)

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)

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)

Knight, J. D. R., Qian B., Baker D., & Kothary R. (2007). Conservation, variability and the modeling of active protein kinases. PloS one. 2(10), e982. Abstract Download: knight07A.pdf (2.64 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)

2006

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)

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)

Baker, M. L., Jiang W., Wedemeyer W. J., Rixon F. J., Baker D., & Chiu W. (2006). Ab initio modeling of the herpesvirus VP26 core domain assessed by CryoEM density. PLoS computational biology. 2(10), e146. Abstract Download: baker06B.pdf (945.92 KB)

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)

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)

Palmer, A. E., Giacomello M., Kortemme T., Hires A. S., Lev-Ram V., Baker D., et al. (2006). Ca2+ indicators based on computationally redesigned calmodulin-peptide pairs. Chemistry & biology. 13(5), 521-30. Abstract Download: palmer06A.pdf (591.03 KB)

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)

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)

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)

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)

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)

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)

Ashworth, J., Havranek J. J., Duarte C. M., Sussman D., Monnat R. J., Stoddard B. L., et al. (2006). Computational redesign of endonuclease DNA binding and cleavage specificity. Nature. 441(7093), 656-9. Abstract Download: ashworth06A.pdf (664.23 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)

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)

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)

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)

Joachimiak, L. A., Kortemme T., Stoddard B. L., & Baker D. (2006). Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface. Journal of molecular biology. 361(1), 195-208. Abstract Download: joachimiak06A.pdf (1.04 MB)

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)

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)

2005

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)

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)

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)

Korkegian, A., Black M. E., Baker D., & Stoddard B. L. (2005). Computational thermostabilization of an enzyme. Science. 308(5723), 857-60. Abstract Download: korkegian05A.pdf (274.59 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)

Jiang, L., Kuhlman B., Kortemme T., & Baker D. (2005). A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins. 58(4), 893-904. Abstract Download: jiang05A.pdf (723.29 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)

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)

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)

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)

Kim, D. E., Chivian D., Malmström L., & Baker D. (2005). Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM. Proteins. 61 Suppl 7, 193-200. Abstract Download: kim05A.pdf (683.21 KB)

Graña, O., Baker D., MacCallum R. M., Meiler J., Punta M., Rost B., et al. (2005). CASP6 assessment of contact prediction. Proteins. 61 Suppl 7, 214-24. Abstract Download: grana05A.pdf (857.44 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)

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)

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)

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)

2004

Misura, K. M. S., Morozov A. V., & Baker D. (2004). Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction. Journal of molecular biology. 342(2), 651-64. Abstract Download: misura04A.pdf (867.48 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)

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)

Morozov, A. V., Kortemme T., Tsemekhman K., & Baker D. (2004). Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proceedings of the National Academy of Sciences of the United States of America. 101(18), 6946-51. Abstract Download: morozov04A.pdf (444.99 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)

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)

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)

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)

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)

Kortemme, T., Kim D. E., & Baker D. (2004). Computational alanine scanning of protein-protein interfaces. Science's STKE. 2004(219), pl2. Abstract Download: kortemme04B.pdf (2.47 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)

Kortemme, T., & Baker D. (2004). Computational design of protein-protein interactions. Current opinion in chemical biology. 8(1), 91-7. Abstract Download: kortemme04A.pdf (204.71 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)

Kortemme, T., Joachimiak L. A., Bullock A. N., Schuler A. D., Stoddard B. L., & Baker D. (2004). Computational redesign of protein-protein interaction specificity. Nature structural & molecular biology. 11(4), 371-9. Abstract Download: kortemme04A.pdf (1.2 MB)

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)

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.

AV, M., KMS M., K T., & D B. (2004). Dimerization Energy Landscapes for Pairs of Ring-Containing Amino Acids in Proteins. Journal of Physical Chemistry B . Abstract Download: morozov04B.pdf (287.34 KB)

2003

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)

Ivankov, D. N., Garbuzynskiy S. O., Alm E., Plaxco K. W., Baker D., & Finkelstein A. V. (2003). Contact order revisited: influence of protein size on the folding rate. Protein science. 12(9), 2057-62. Abstract Download: ivankov03A.pdf (146.63 KB)

Boulanger, M. J., Bankovich A. J., Kortemme T., Baker D., & Garcia C. K. (2003). Convergent mechanisms for recognition of divergent cytokines by the shared signaling receptor gp130. Molecular cell. 12(3), 577-89. Abstract Download: boulanger03A.pdf (784.25 KB)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

Hazbun, T. R., Malmström L., Anderson S., Graczyk B. J., Fox B., Riffle M., et al. (2003). Assigning function to yeast proteins by integration of technologies. Molecular cell. 12(6), 1353-65. Abstract Download: hazbun03A.pdf (390.65 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)

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)

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)

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)

Chivian, D., Robertson T., Bonneau R., & Baker D. (2003). Ab initio methods. Methods of biochemical analysis. 44, 547-57. Download: chivan03A.pdf (5.89 MB)

Chivian, D., Kim D. E., Malmström L., Bradley P., Robertson T., Murphy P., et al. (2003). Automated prediction of CASP-5 structures using the Robetta server. Proteins. 53 Suppl 6, 524-33. Abstract Download: chivian03A.pdf (501.15 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)

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)

2002

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)

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)

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)

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)

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)

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)

Schonbrun, J., Wedemeyer W. J., & Baker D. (2002). Protein structure prediction in 2002.. Current opinion in structural biology. 12(3), 348-54. Abstract

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)

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)

Kuhlman, B., O'Neill J. W., Kim D. E., Zhang K. Y. J., & Baker D. (2002). Accurate computer-based design of a new backbone conformation in the second turn of protein L. Journal of molecular biology. 315(3), 471-7. Abstract Download: kuhlman02A.pdf (281.28 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)

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)

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)

Schlosshauer, M., & Baker D. (2002). Ageneral expressionforbimolecularassociationrates withorientational constraints. Physical Chemistry B. Download: schlosshauer02A.pdf (250.05 KB)

2001

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)

Baker, D., & Sali A. (2001). Protein structure prediction and structural genomics.. Science (New York, N.Y.). 294(5540), 93-6. Abstract

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)

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)

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)

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)

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)

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)

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)

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)

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., Alm E. J., Baker D., & Horwich A. L. (2001). Mechanisms of protein folding.. Current opinion in structural biology. 11(1), 70-82. 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)

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., & 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)

2000

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)

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)

Baker, D. (2000). A surprising simplicity to protein folding. Nature. 405(6782), 39-42. Abstract Download: baker00A.pdf (853.11 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)

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)

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)

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)

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

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)

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)

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)

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)

1999

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)

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)

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)

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)

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)

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)

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)

Baker, D., & DeGrado W. F. (1999). Engineering and design. Current opinion in structural biology. 9(4), 485-6.

Alm, E., & Baker D. (1999). Matching theory and experiment in protein folding.. Current opinion in structural biology. 9(2), 189-96. Abstract

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

1998

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)

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)

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

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)

Baker, D. (1998). Metastable states and folding free energy barriers.. Nature structural biology. 5(12), 1021-4.

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)

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)

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)

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)

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)

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)

1997

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)

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)

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)

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

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)

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)

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)

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)

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)

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)

1996

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)

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)

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)

1995

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)

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)

1993

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)

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)

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)

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)

1992

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)

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

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)

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)

1988

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)

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)

This publication list was extracted from the Baker lab website at: http://depts.washington.edu/bakerpg/drupal/biblio

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