Publications

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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)
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)
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
Bonneau, R., & Baker D. (2001).  Ab initio protein structure prediction: progress and prospects.. Annual review of biophysics and biomolecular structure. 30, 173-89. Abstract
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)
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)
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
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)
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)
Schlosshauer, M., & Baker D. (2002).  Ageneral expressionforbimolecularassociationrates withorientational constraints. Physical Chemistry B.  Download: schlosshauer02A.pdf (250.05 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)
Li, J., Shinjo M., Matsumura Y., Morita M., Baker D., Ikeguchi M., et al. (2007).  An alpha-helical burst in the src SH3 folding pathway. Biochemistry. 46(17), 5072-82. Abstract  Download: li07A.pdf (493.42 KB)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)