Publications

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Sanowar, S., Singh P., Pfuetzner R. A., AndrĂ© 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)
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)
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)
Bonneau, R., Strauss C. E., & Baker D. (2001).  Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation. Proteins. 43(1), 1-11. Abstract  Download: bonneau01A.pdf (554.67 KB)
Krieger, E., Joo K., Lee J., Lee J., Raman S., Thompson J., et al. (2009).  Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins. 77 Suppl 9, 114-22. Abstract  Download: krieger09A.pdf (646.49 KB)
Ramelot, T. A., Raman S., Kuzin A. P., Xiao R., Ma L. - C., Acton T. B., et al. (2009).  Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study. Proteins. 75(1), 147-67. Abstract  Download: ramelot09A.pdf (790.67 KB)
Qian, B., Ortiz A. R., & Baker D. (2004).  Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. Proceedings of the National Academy of Sciences of the United States of America. 101(43), 15346-51. Abstract  Download: qian04A.pdf (573.21 KB)
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)
Wang, C., Schueler-Furman O., & Baker D. (2005).  Improved side-chain modeling for protein-protein docking. Protein science. 14(5), 1328-39. Abstract  Download: wang05A.pdf (736.4 KB)
Simons, K. T., Ruczinski I., Kooperberg C., Fox B. A., Bystroff C., & Baker D. (1999).  Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins. 34(1), 82-95. Abstract  Download: simons98A.pdf (313.04 KB)
Tsai, J., Bonneau R., Morozov A. V., Kuhlman B., Rohl C. A., & Baker D. (2003).  An improved protein decoy set for testing energy functions for protein structure prediction. Proteins. 53(1), 76-87. Abstract  Download: Tsai03A.pdf (376.65 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)
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
Bradley, P., & Baker D. (2006).  Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation. Proteins. 65(4), 922-9. Abstract  Download: bradley06A.pdf (837.59 KB)
Grantcharova, V. P., Riddle D. S., Santiago J. V., & Baker D. (1998).  Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain. Nature structural biology. 5(8), 714-20. Abstract  Download: grantcharova98A.pdf (833.81 KB)