Publications

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2012
Kellogg, E. H., Lange O. F., & Baker D. (2012).  Evaluation and optimization of discrete state models of protein folding.. The journal of physical chemistry. B. 116(37), 11405-13. Abstract
Baxter, S., Lambert A. R., Kuhar R., Jarjour J., Kulshina N., Parmeggiani F., et al. (2012).  Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases.. Nucleic acids research. 40(16), 7985-8000. Abstract
Richter, F., Blomberg R., Khare S. D., Kiss G., Kuzin A. P., Smith A. J. T., et al. (2012).  Computational design of catalytic dyads and oxyanion holes for ester hydrolysis.. Journal of the American Chemical Society. 134(39), 16197-206. Abstract
Koga, N., Tatsumi-Koga R., Liu G., Xiao R., Acton T. B., Montelione G. T., et al. (2012).  Principles for designing ideal protein structures.. Nature. 491(7423), 222-7. Abstract  Download: nature11600.pdf (2.17 MB)
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)
Althoff, E. A., Wang L., Jiang L., Giger L., Lassila J. K., Wang Z., et al. (2012).  Robust design and optimization of retroaldol enzymes.. Protein science : a publication of the Protein Society. 21(5), 717-26. Abstract
Lange, O. F., & Baker D. (2012).  Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation.. Proteins. 80(3), 884-95. Abstract
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
Khersonsky, O., Kiss G., Röthlisberger D., Dym O., Albeck S., Houk K. N., et al. (2012).  Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59.. Proceedings of the National Academy of Sciences of the United States of America. 109(26), 10358-63. Abstract
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
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
Lange, O. F., Rossi P., Sgourakis N. G., Song Y., Lee H. - W., Aramini J. M., et al. (2012).  Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples.. Proceedings of the National Academy of Sciences of the United States of America. 109(27), 10873-8. Abstract
Azoitei, M. L., Ban Y. - E. A., Julien J. - P., Bryson S., Schroeter A., Kalyuzhniy O., et al. (2012).  Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope. Journal of molecular biology. 415(1), 175-92. Abstract  Download: azoitei12A.pdf (1.79 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)
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)
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)
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)
Rosato, A., Aramini J. M., Arrowsmith C., Bagaria A., Baker D., Cavalli A., et al. (2012).  Blind testing of routine, fully automated determination of protein structures from NMR data. Structure. 20(2), 227-36. Abstract
Khare, S. D., Kipnis Y., Greisen P. J., Takeuchi R., Ashani Y., Goldsmith M., et al. (2012).  Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. Nature chemical biology. Abstract  Download: khare12A.pdf (1.14 MB)
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
Fleishman, S. J., & Baker D. (2012).  Role of the biomolecular energy gap in protein design, structure, and evolution.. Cell. 149(2), 262-73. Abstract
Eiben, C. B., Siegel J. B., Bale J. B., Cooper S., Khatib F., Shen B. W., et al. (2012).  Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nature biotechnology. 30(2), 190-2. Abstract  Download: eiben12A.pdf (552.17 KB)
King, N. P., Sheffler W., Sawaya M. R., Vollmar B. S., Sumida J. P., André I., et al. (2012).  Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science. Abstract  Download: king12A.pdf (1.36 MB)
Loquet, A., Sgourakis N. G., Gupta R., Giller K., Riedel D., Goosmann C., et al. (2012).  Atomic model of the type III secretion system needle. Nature. Abstract  Download: sgourakis12A.pdf (1015.62 KB)
2011
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
Bouvignies, G., Vallurupalli P., Hansen F. D., Correia B. E., Lange O., Bah A., et al. (2011).  Solution structure of a minor and transiently formed state of a T4 lysozyme mutant. Nature. 477(7362), 111-4. Abstract  Download: bouvignies11A.pdf (1023.45 KB)
Azoitei, M. L., Correia B. E., Ban Y. - E. A., Carrico C., Kalyuzhniy O., Chen L., et al. (2011).  Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold. Science. 334(6054), 373-6. Abstract  Download: azoitei11A.pdf (2.01 MB)
Khatib, F., DiMaio F., Cooper S., Kazmierczyk M., Gilski M., Krzywda S., et al. (2011).  Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nature structural & molecular biology. 18(10), 1175-7. Abstract  Download: khatib11A.pdf (893.7 KB)
Khatib, F., Cooper S., Tyka M. D., Xu K., Makedon I., Popovic Z., et al. (2011).  Algorithm discovery by protein folding game players.. Proceedings of the National Academy of Sciences of the United States of America. Abstract  Download: Khatib11B.pdf (2.4 MB)
Fleishman, S. J., Whitehead T. A., Ekiert D. C., Dreyfus C., Corn J. E., Strauch E. - M., et al. (2011).  Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science. 332(6031), 816-21. Abstract  Download: fleishman11B.pdf (643.74 KB)
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)
DiMaio, F., Terwilliger T. C., Read R. J., Wlodawer A., Oberdorfer G., Wagner U., et al. (2011).  Improved molecular replacement by density- and energy-guided protein structure optimization. Nature. Abstract  Download: dimaio11A.pdf (972.77 KB)
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)
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)
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)
Brzovic, P. S., Heikaus C. C., Kisselev L., Vernon R., Herbig E., Pacheco D., et al. (2011).  The acidic transcription activator Gcn4 binds the mediator subunit Gal11/Med15 using a simple protein interface forming a fuzzy complex. Molecular cell. 44(6), 942-53. Abstract  Download: brzovic11A.pdf (1.14 MB)
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)
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)