Wagner, J. R., J. Sorensen, N. Hensley, C. Wong, C. Zhu, T. Perison, and R. E. Amaro. 2017. POVME 3.0: Software for Mapping Binding Pocket Flexibility. J Chem Theory Comput 13:4584-4592.

P. Barros, E., R. D. Malmstrom, K. Nourbakhsh, J. C. Del Rio, A. P. Kornev, S. S. Taylor, and R. E. Amaro. 2017. Electrostatic Interactions as Mediators in the Allosteric Activation of Protein Kinase A RIα. Biochemistry 56:1536-1545.

Hirakis, S. P., R. D. Malmstrom, and R. E. Amaro. 2017. Molecular Simulations Reveal an Unresolved Conformation of the Type IA Protein Kinase A Regulatory Subunit and Suggest Its Role in the cAMP Regulatory Mechanism. Biochemistry 56:3885-3888.

Cheng, K. J., O. Demir, and R. E. Amaro. 2017. A Comparative Study of the Structural Dynamics of Four Terminal Uridylyl Transferases. Genes (Basel) 8.

Swift, R. V., S. A. Jusoh, T. L. Offutt, E. S. Li, and R. E. Amaro. 2016. Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles. J Chem Inf Model 56:830-842.

Schiffer, J. M., V. A. Feher, R. D. Malmstrom, R. Sida, and R. E. Amaro. 2016. Capturing Invisible Motions in the Transition from Ground to Rare Excited States of T4 Lysozyme L99A. Biophys J 111:1631-1640.

Buffalo, C. Z., A. J. Bahn-Suh, S. P. Hirakis, T. Biswas, R. E. Amaro, V. Nizet, and P. Ghosh. 2016. Conserved patterns hidden within group A Streptococcus M protein hypervariability recognize human C4b-binding protein. Nat Microbiol 1:16155.

Hirakis, S., B. Boras, L. Votapka, R. Malmstrom, A. McCulloch, and R. Amaro. 2015. Bridging scales through multiscale modeling: a case study on protein kinase A. Frontiers in Physiology 6.

Chen, E., R. V. Swift, N. Alderson, V. A. Feher, G. S. Feng, and R. E. Amaro. 2014. Computation-guided discovery of influenza endonuclease inhibitors. ACS Med Chem Lett 5:61-64.

Ieong, P. U., J. Sørensen, P. L. Vemu, C. W. Wong, Ö. Demir, N. P. Williams, J. Wang, D. Crawl, R. V. Swift, R. D. Malmstrom, I. Altintas, and R. E. Amaro. 2014. Progress towards Automated Kepler Scientific Workflows for Computer-aided Drug Discovery and Molecular Simulations. Procedia Computer Science 29:1745-1755.

Park, J., L. Czapla, and R. E. Amaro. 2013. Molecular Simulations of Aromatase Reveal New Insights Into the Mechanism of Ligand Binding. Journal of Chemical Information and Modeling 53:2047-2056.