Publications

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2010
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)
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)
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)
2011
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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
2012
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)
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)
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)
Fleishman, S. J., & Baker D. (2012).  Role of the biomolecular energy gap in protein design, structure, and evolution.. Cell. 149(2), 262-73. Abstract
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
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)
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
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)
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)
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)
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)
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)
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
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
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
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
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
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
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
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)
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)
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
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
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