James J. Havranek, Ph.D.

James Havranek
Assistant Professor

Biochemistry and Molecular Biophysics

Publications (PubMed / NIH)

Office: 1914 South Building
Phone: 314-362-2594
Email: jjhavranek(at)wustl.edu


The Havranek lab studies specificity in protein-DNA and protein-peptide interactions using computational and experimental approaches. We develop and apply computational protein design alogrithms to generate useful molecular tools. Current projects include the development of protein probes for single molecule peptide sequencing and engineering Cre recombinase for genome editing applications.

havranek PastedGraphic-1


  • Chang Y.K., Srivastava Y., Hu C., Joyce A., Yang X., Zuo Z., Havranek J.J., Stormo G.D., and Jauch R.
    Quantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq.
    Nucleic Acids Res. (2017) (Abstract)

  • Zhang, C., Myers, C.A., Qi, Z., Mitra, R.D., Corbo, J.C. and Havranek, J.J. Redesign of the monomer-monomer interface of Cre recombinase yields an obligate heterotetrameric complex. Nucleic Acids Res. 43:9076-9085 (2015). [Abstract]

  • Sasaki, Y., Margolin, Z., Borgo, B., Havranek, J.J. and Milbrandt, J. Characterization of Leber’s congenital amaurosis-associated NMNAT1 mutants. J Biol Chem 290:17228-17238 (2015). [Abstract]

  • Joyce, A.P., Zhang, C., Bradley, P. and Havranek, J.J. Structure-based modeling of protein: DNA specificity. Brief Funct Genomics 14:39-49 (2015). [Abstract]

  • Borgo, B. and Havranek, J.J. Motif-directed redesign of enzyme specificity. Protein Science 23:312-320 (2014). [Abstract]

  • Lyskov, S., Chou, F.C., Conchuir, S.O., Der, B.S., Drew, K., Kuroda, D., Xu, J., Weitzner, B.D., Renfrew, P.D., Sripakdeevong, P., borgo, B., Havranek, J.J., Kuhlman, B., Kortemme, T., Bonneau, R., Gray, J.J. and Das, R. Serverification of molecular modeling applications: The Rosetta online server that includes everyone (ROSIE). PLoS One 8:e63906.(2013). [Abstract]

  • Leaver-Fay, A., O’Meara, M.J., Tyka, M., Jacak, R., Song, Y., Kellogg, E.H., Thompson, J., Davis, I.W., Pache, R.A., Lyskov, S., Gray, J.J., Kortemme, T., Richardson, J.S., Havranek, J.J. Snoeyink, J., Baker, D. and Kuhlman, B. Scientific-benchmarks for guiding macromolecular energy function improvement. Methods Enzymol 523:109-143.(2013). [Abstract]

  • Tang, Y.T., Gao, R., Havranek, J.J., Groisman, E.A., Stock, A.M. and Marshall, G.R. Inhibition of bacterial virulence: Drug-like molecules targeting the Salmonella entrica PhoP response regulator. Chem Biol Drug Des. 79:1007-1017. (2012). [Abstract]

  • Borgo, B. and Havranek, J.J. Automated selection of stabilizing mutations in designed and natural proteins. PNAS 109:1494-1499.(2012). [Abstract]

  • Leaver-Fay, A., Tyka, M., Lewis, S.M., Lange, O.F., Thompson, J., Jacak, R., Kaufman, K., Renfrew, P.D., Smith, C.A., Sheffler, W., Davis, I.W., Cooper, S., Treuille, A., Mandell, D.J., Richter, F., Ban, Y.E., Fleishman, S.J., Corn, J.E., Kim, D.E., Lyskov, S., Berrondo, M., Mentzer, S., Popovic, Z., Havranek, J.J., Karanicolas, J., Das, R., Meiler, J., Kortemme, T., Gray, J.J., Kuhlman, B., Baker, B. and Bradley, P. ROSETTA3: An object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol. 487:545-574.(2011). [Abstract]