Publications
2020
Lowegard, A. U., Frenkel, M. S., Holt, G. T., Jou, J. D., Ojewole, A. A. & Donald, B. R. Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD:KRas protein-protein interface. PLOS Computational Biology 16.
Jou, J. D., Holt, G. T., Lowegard, A. U. & Donald, B. R. Minimization-Aware Recursive K*: A novel, provable algorithm that accelerates ensemble-based protein design and provably approximates the energy landscape. Journal of Computational Biology 27, 550–564.
2019
Holt, G. T., Jou, J. D., Gill, N. P., Lowegard, A. U., Martin, J. W., Madden, D. R., et al. Computational analysis of energy landscapes reveals dynamic features that contribute to binding of inhibitors to CFTR-associated ligand. The Journal of Physical Chemistry B 123, 10441–10455.
Reeve, S. M., Si, D., Krucinska, J., Yan, Y., Viswanathan, K., Wang, S., et al. Toward broad spectrum dihydrofolate reductase inhibitors targeting trimethoprim resistant enzymes identified in clinical isolates of methicillin resistant Staphylococcus aureus. ACS Infectious Diseases 5, 1896–1906.
2018
Moeyaert, B., Holt, G., Madangopal, R., Perez-Alvarez, A., Fearey, B. C., Trojanowski, N. F., et al. Improved methods for marking active neuron populations. Nature Communications 9, 4440.
Hallen, M. A., Martin, J. W., Ojewole, A., Jou, J. D., Lowegard, A. U., Frenkel, M. S., et al. OSPREY 3.0: Open-source protein redesign for you, with powerful new features. Journal of Computational Chemistry 39, 2494–2507.
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