Publications

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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)
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)
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)
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)
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)
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., 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)
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)
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)
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)
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)
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)