Publications

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Wang, C., Schueler-Furman O., Andre I., London N., Fleishman S. J., Bradley P., et al. (2007).  RosettaDock in CAPRI rounds 6-12. Proteins. 69(4), 758-63. Abstract  Download: wang07B.pdf (214.39 KB)
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Stankunas, K., Bayle H. J., Havranek J. J., Wandless T. J., Baker D., Crabtree G. R., et al. (2007).  Rescue of degradation-prone mutants of the FK506-rapamycin binding (FRB) protein with chemical ligands. Chembiochem : a European journal of chemical biology. 8(10), 1162-9. Abstract  Download: stankunas07A.pdf (579.3 KB)
Sood, V. D., & Baker D. (2006).  Recapitulation and design of protein binding peptide structures and sequences. Journal of molecular biology. 357(3), 917-27. Abstract  Download: sood06A.pdf (497.29 KB)
Song, G., Lazar G. A., Kortemme T., Shimaoka M., Desjarlais J. R., Baker D., et al. (2006).  Rational design of intercellular adhesion molecule-1 (ICAM-1) variants for antagonizing integrin lymphocyte function-associated antigen-1-dependent adhesion. The Journal of biological chemistry. 281(8), 5042-9. Abstract  Download: song06A.pdf (277.35 KB)
Sheffler, W., & Baker D. (2010).  RosettaHoles2: a volumetric packing measure for protein structure refinement and validation. Protein science. 19(10), 1991-5. Abstract  Download: sheffler10A.pdf (327.06 KB)
Sheffler, W., & Baker D. (2009).  RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation. Protein science. 18(1), 229-39. Abstract  Download: sheffler09A.pdf (503.42 KB)
Schlosshauer, M., & Baker D. (2004).  Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness. Protein science. 13(6), 1660-9. Abstract  Download: schlosshauer04A.pdf (185.7 KB)
Saunders, C. T., & Baker D. (2005).  Recapitulation of protein family divergence using flexible backbone protein design. Journal of molecular biology. 346(2), 631-44. Abstract  Download: saundersa05A.pdf (639.35 KB)
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Ruohola, H., Bremer K. A., Baker D., Swedlow J. R., Jan L. Y., & Jan Y. N. (1991).  Role of neurogenic genes in establishment of follicle cell fate and oocyte polarity during oogenesis in Drosophila.. Cell. 66(3), 433-49. Abstract  Download: ruoholaa91.pdf (0 bytes)
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Qiu, J., Sheffler W., Baker D., & Noble W. S. (2008).  Ranking predicted protein structures with support vector regression. Proteins. 71(3), 1175-82. Abstract  Download: qiu08A.pdf (320.82 KB)
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Meiler, J., & Baker D. (2003).  Rapid protein fold determination using unassigned NMR data. Proceedings of the National Academy of Sciences of the United States of America. 100(26), 15404-9. Abstract  Download: meiler03B.pdf (593 KB)
Meiler, J., & Baker D. (2006).  ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins. 65(3), 538-48. Abstract  Download: meiler06A.pdf (760.02 KB)
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Luo, B. - H., Karanicolas J., Harmacek L. D., Baker D., & Springer T. A. (2009).  Rationally designed integrin beta3 mutants stabilized in the high affinity conformation. The Journal of biological chemistry. 284(6), 3917-24. Abstract  Download: luo09A.pdf (673.21 KB)
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)
Larson, S. M., Ruczinski I., Davidson A. R., Baker D., & Plaxco K. W. (2002).  Residues participating in the protein folding nucleus do not exhibit preferential evolutionary conservation. Journal of molecular biology. 316(2), 225-33. Abstract  Download: larson02A.pdf (213.29 KB)
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
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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)
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Jardine, J., Julien J. - P., Menis S., Ota T., Kalyuzhniy O., McGuire A., et al. (2013).  Rational HIV immunogen design to target specific germline B cell receptors.. Science (New York, N.Y.). 340(6133), 711-6. Abstract
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Han, K. F., & Baker D. (1995).  Recurring local sequence motifs in proteins. Journal of molecular biology. 251(1), 176-87. Abstract  Download: han95A.pdf (297.22 KB)
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Gu, H., Doshi N., Kim D. E., Simons K. T., Santiago J. V., Nauli S., et al. (1999).  Robustness of protein folding kinetics to surface hydrophobic substitutions. Protein science. 8(12), 2734-41. Abstract  Download: gu99A.pdf (368.14 KB)
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Fleishman, S. J., & Baker D. (2012).  Role of the biomolecular energy gap in protein design, structure, and evolution.. Cell. 149(2), 262-73. Abstract
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)
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DiMaio, F., Tyka M. D., Baker M. L., Chiu W., & Baker D. (2009).  Refinement of protein structures into low-resolution density maps using rosetta. Journal of molecular biology. 392(1), 181-90. Abstract  Download: dimaio09A.pdf (1.54 MB)
Davis, I. W., & Baker D. (2009).  RosettaLigand docking with full ligand and receptor flexibility. Journal of molecular biology. 385(2), 381-92. Abstract  Download: davis09B.pdf (1.36 MB)
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Bradley, P., Chivian D., Meiler J., Misura K. M. S., Rohl C. A., Schief W. R., et al. (2003).  Rosetta predictions in CASP5: successes, failures, and prospects for complete automation. Proteins. 53 Suppl 6, 457-68. Abstract  Download: bradley03A.pdf (1.05 MB)
Bonneau, R., Tsai J., Ruczinski I., Chivian D., Rohl C., Strauss C. E., et al. (2001).  Rosetta in CASP4: progress in ab initio protein structure prediction. Proteins. Suppl 5, 119-26. Abstract  Download: bonneau01C.pdf (682.51 KB)
Bergeron, J. R. C., Worrall L. J., Sgourakis N. G., DiMaio F., Pfuetzner R. A., Felise H. B., et al. (2013).  A Refined Model of the Prototypical Salmonella SPI-1 T3SS Basal Body Reveals the Molecular Basis for Its Assembly.. PLoS pathogens. 9(4), e1003307. Abstract
Baker, D., Hicke L., Rexach M., Schleyer M., & Schekman R. (1988).  Reconstitution of SEC gene product-dependent intercompartmental protein transport. Cell. 54(3), 335-44. Abstract  Download: baker88.pdf (3.33 MB)
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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