Publications

Found 339 results

2014
Baker, D. (2014).  Protein folding, structure prediction and design.. Biochemical Society transactions. 42(2), 225-9. Abstract  Download: Baker_BiochemSocTrans_2014.pdf (295.67 KB)
Thyme, S., & Baker D. (2014).  Redesigning the Specificity of Protein-DNA Interactions with Rosetta.. Methods in molecular biology (Clifton, N.J.). 1123, 265-82. Abstract  Download: Thyme_2014.pdf (413.9 KB)
King, C., Garza E. N., Mazor R., Linehan J. L., Pastan I., Pepper M., et al. (2014).  Removing T-cell epitopes with computational protein design.. Proceedings of the National Academy of Sciences of the United States of America. Abstract  Download: King_PNAS_2014A.pdf (960 KB)
Wijma, H. J., Floor R. J., Jekel P. A., Baker D., Marrink S. J., & Janssen D. B. (2014).  Computationally designed libraries for rapid enzyme stabilization.. Protein engineering, design & selection : PEDS. 27(2), 49-58. Abstract  Download: Wijma_PEDS_2014.pdf (953.89 KB)
2013
Cooper, S., Khatib F., & Baker D. (2013).  Increasing public involvement in structural biology. Structure (London, England : 1993). 21(9), 1482-4. Abstract  Download: Cooper13L.pdf (512 KB)
Kamisetty, H., Ovchinnikov S., & Baker D. (2013).  Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era.. Proceedings of the National Academy of Sciences of the United States of America. 110(39), 15674-9. Abstract
Procko, E., Hedman R., Hamilton K., Seetharaman J., Fleishman S. J., Su M., et al. (2013).  Computational design of a protein-based enzyme inhibitor.. Journal of molecular biology. 425(18), 3563-75. Abstract  Download: Procko13.pdf (2.98 MB)
Song, Y., DiMaio F., Yu-Ruei Wang R., Kim D., Miles C., Brunette T., et al. (2013).  High-resolution comparative modeling with RosettaCM.. Structure (London, England : 1993). 21(10), 1735-42. Abstract
Kiss, G., Celebi-Ölçüm N., Moretti R., Baker D., & Houk K. N. (2013).  Computational enzyme design. Angewandte Chemie (International ed. in English). 52(22), 5700-25. Abstract
DiMaio, F., Zhang J., Chiu W., & Baker D. (2013).  Cryo-EM model validation using independent map reconstructions. Protein science : a publication of the Protein Society. 22(6), 865-8. Abstract  Download: DiMaio_pro2267_13Q.pdf (225.1 KB)
Strauch, E. - M., Fleishman S. J., & Baker D. (2013).  Computational design of a pH-sensitive IgG binding protein. Proceedings of the National Academy of Sciences of the United States of America. Abstract  Download: Strauch-1313605111_PNAS_13W.pdf (1.32 MB)
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
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
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
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
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)
Gordon, S. R., Stanley E. J., Wolf S., Toland A., Wu S. J., Hadidi D., et al. (2012).  Computational Design of an α-gliadin Peptidase. Journal of the American Chemical Society. 134(50), 20513-20. Abstract  Download: Gordon12E.pdf (2.05 MB)
2011
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)