Center-Authored Papers

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Triazines
Murphy PM, Bolduc JM, Gallaher JL, Stoddard BL, 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
Transfection
McBeth C, Seamons A, Pizarro JC, Fleishman SJ, Baker D, Kortemme T, Goverman JM, Strong RK.  2008.  A new twist in TCR diversity revealed by a forbidden alphabeta TCR.. Journal of molecular biology. 375(5):1306-19. Abstract
Thymus Gland
McBeth C, Seamons A, Pizarro JC, Fleishman SJ, Baker D, Kortemme T, Goverman JM, Strong RK.  2008.  A new twist in TCR diversity revealed by a forbidden alphabeta TCR.. Journal of molecular biology. 375(5):1306-19. Abstract
Thermodynamics
Thyme SB, Jarjour J, Takeuchi R, Havranek JJ, Ashworth J, Scharenberg AM, Stoddard BL, Baker D.  2009.  Exploitation of binding energy for catalysis and design.. Nature. 461(7268):1300-4. Abstract
Surface Plasmon Resonance
Azoitei ML, Correia BE, Ban Y-EA, Carrico C, Kalyuzhniy O, Chen L, Schroeter A, Huang P-S, McLellan JS, Kwong PD et al..  2011.  Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold.. Science (New York, N.Y.). 334(6054):373-6. Abstract
McBeth C, Seamons A, Pizarro JC, Fleishman SJ, Baker D, Kortemme T, Goverman JM, Strong RK.  2008.  A new twist in TCR diversity revealed by a forbidden alphabeta TCR.. Journal of molecular biology. 375(5):1306-19. Abstract
Substrate Specificity
Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, St Clair JL, Gallaher JL, Hilvert D, Gelb MH, Stoddard BL et al..  2010.  Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction.. Science (New York, N.Y.). 329(5989):309-13. Abstract
Thyme SB, Song Y, Brunette TJ, Szeto MD, Kusak L, Bradley P, Baker D.  2014.  Massively parallel determination and modeling of endonuclease substrate specificity.. Nucleic acids research. 42(22):13839-52. Abstract
Thyme SB, Jarjour J, Takeuchi R, Havranek JJ, Ashworth J, Scharenberg AM, Stoddard BL, Baker D.  2009.  Exploitation of binding energy for catalysis and design.. Nature. 461(7268):1300-4. Abstract
Ashworth J, Taylor GK, Havranek JJ, Quadri AS, Stoddard BL, Baker D.  2010.  Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs.. Nucleic acids research. 38(16):5601-8. Abstract
Murphy PM, Bolduc JM, Gallaher JL, Stoddard BL, 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
Stereoisomerism
Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, St Clair JL, Gallaher JL, Hilvert D, Gelb MH, Stoddard BL et al..  2010.  Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction.. Science (New York, N.Y.). 329(5989):309-13. Abstract
Spodoptera
McBeth C, Seamons A, Pizarro JC, Fleishman SJ, Baker D, Kortemme T, Goverman JM, Strong RK.  2008.  A new twist in TCR diversity revealed by a forbidden alphabeta TCR.. Journal of molecular biology. 375(5):1306-19. Abstract
Software
Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew DP, Smith CA, Sheffler W et al..  2011.  ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.. Methods in enzymology. 487:545-74. Abstract
Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, St Clair JL, Gallaher JL, Hilvert D, Gelb MH, Stoddard BL et al..  2010.  Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction.. Science (New York, N.Y.). 329(5989):309-13. Abstract
Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Andre I, Thompson J, Havranek JJ, Das R, Bradley P, Baker D.  2010.  Rosetta in CAPRI rounds 13-19.. Proteins. 78(15):3212-8. Abstract
Shared Resources
Brzovic PS, Heikaus CC, Kisselev L, Vernon R, Herbig E, Pacheco D, Warfield L, Littlefield P, Baker D, Klevit RE 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
Boissel S, Jarjour J, Astrakhan A, Adey A, Gouble A, Duchateau P, Shendure J, Stoddard BL, Certo MT, Baker D et al..  2014.  megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering.. Nucleic acids research. 42(4):2591-601. Abstract
Sequence Analysis, DNA
Thyme SB, Song Y, Brunette TJ, Szeto MD, Kusak L, Bradley P, Baker D.  2014.  Massively parallel determination and modeling of endonuclease substrate specificity.. Nucleic acids research. 42(22):13839-52. Abstract
September 2013
Tinberg CE, Khare SD, Dou J, Doyle L, Nelson JW, Schena A, Jankowski W, Kalodimos CG, Johnsson K, Stoddard BL et al..  2013.  Computational design of ligand-binding proteins with high affinity and selectivity.. Nature. 501(7466):212-6. Abstract
Sensitivity and Specificity
McBeth C, Seamons A, Pizarro JC, Fleishman SJ, Baker D, Kortemme T, Goverman JM, Strong RK.  2008.  A new twist in TCR diversity revealed by a forbidden alphabeta TCR.. Journal of molecular biology. 375(5):1306-19. Abstract
Selection, Genetic
McBeth C, Seamons A, Pizarro JC, Fleishman SJ, Baker D, Kortemme T, Goverman JM, Strong RK.  2008.  A new twist in TCR diversity revealed by a forbidden alphabeta TCR.. Journal of molecular biology. 375(5):1306-19. Abstract
Scientific Imaging Core Facility
Brzovic PS, Heikaus CC, Kisselev L, Vernon R, Herbig E, Pacheco D, Warfield L, Littlefield P, Baker D, Klevit RE 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
Saccharomyces cerevisiae Proteins
Brzovic PS, Heikaus CC, Kisselev L, Vernon R, Herbig E, Pacheco D, Warfield L, Littlefield P, Baker D, Klevit RE 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
Saccharomyces cerevisiae
Thyme SB, Jarjour J, Takeuchi R, Havranek JJ, Ashworth J, Scharenberg AM, Stoddard BL, Baker D.  2009.  Exploitation of binding energy for catalysis and design.. Nature. 461(7268):1300-4. Abstract