James J. Havranek, Ph.D.

Assistant Professor
Biochemistry and Molecular Biophysics

Computational and Systems Biology Program
Biochemistry, Biophysics, and Structural Biology Program

  • 314-362-2535

  • 314-362-2594

  • 8232

  • South Building, Room 1914

  • jjhavranek@wustl.edu

  • http://www.genetics.wustl.edu/jhlab

  • Molecular specificity, Computational Protein Design, Synthetic Biology, Protein-DNA Interactions

  • Structural modeling, experimental characterization, and engineering of protein-DNA interactions

Research Abstract:

The Havranek group uses computational protein design and directed evolution to develop molecular tools for high-throughput peptide sequencing and novel genome engineering applications. We have a long-standing interest in studying the specificity of macromolecular interactions, particularly protein:DNA interactions, both computationally and experimentally.

Selected Publications:

Borgo B and Havranek JJ. Computer-aided design of a catalyst for Edman degradation utilizing substrate-assisted catalysis. Protein Sci. 2015 (available online).

Joyce AP, Zhang C, Bradley P, and Havranek JJ. Structure-based modeling of protein:DNA specificity. Briefings in Functional Genomics. 2014 (available online)

Borgo B and Havranek JJ. Motif-directed redesign of enzyme specificity. Protein Sci. 2014 23(3): 312-320.

Borgo B and Havranek JJ. Automated selection of stabilizing mutations in designed and natural proteins. Proc. Natl. Acad. Sci. 2012 109(5): 1494-1499.

Havranek JJ. Specificity in Computational Protein Design. J. Biol. Chem. 2010 285(41): 31095-31099.

Havranek JJ and Baker D. Motif-directed flexible backbone design of functional interactions. Protein Sci. 2009 18(6):1293-1305.

Ashworth JA , Havranek JJ, Duarte CM, Sussman D, Monnat RJ, Stoddard BL, Baker D. Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 441 2006 7093: 656-659.

Morozov AV, Havranek JJ, Baker D, Siggia ED. Protein-DNA binding specificity predictions with structural models. Nuc. Acids Res. 2005 33(18): 5781-5798.

Havranek JJ, Duarte CM and Baker D. A Simple Physical Model for the Prediction and Design of Protein-DNA Interactions. J. Mol. Biol. 2004 344(1): 59-70.

Havranek JJ and Harbury PB. Automated Design of Specificity in Molecular Recognition. Nature Struct. Biol. 2003 10(1): 45-52.

Last Updated: 1/16/2015 9:51:23 AM

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