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Rommie Amaro



Select Publications

  • Casalino, L., Gaieb, Z., Goldsmith, J.A., Hjorth, C.K., Dommer, A.C., Harbison, A.M., Fogarty, C.A., Barros, E.P., Taylor, B.C., McLellan, J.S., Fadda, E., Amaro, R.E., “Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein,” ACS Cent. Sci. 6, 1722–1734 (2020). doi: 10.1021/acscentsci.0c01056
  • Wassman, C.D., Baronio, R., Demir, .., Wallentine, B.D., Chen, C-K., Hall, L.V., Salehi, F., Lin, D-W., Chung, B.P., Hatfield, G.W., Chamberlin, A.R., Luecke, H., Lathrop, R.H., Kaiser, P., Amaro, R.E. “Computational Identification of a Transiently Open L1/S3 Pocket for p53 Cancer Mutant Reactivation”, Nature Comm. 4, 1407 (2013). doi:10.1038/ncomms2361.
  • Durrant, J.D., Kochanek, S.E., Casalino, L., Ieong, P.U., Dommer, A.C., Amaro, R.E., “Mesoscale All- Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism”, ACS Cent. Sci. 6, 189–196 (2020).
  • Kim, S.H., Kearns, F.L., Rosenfeld, M., Casalino, L., Papanikolas, M.J., Simmerling, C., Amaro, R.E., and Freeman, R., GlycoGrip: Cell Surface-Inspired Universal Sensor for Betacoronaviruses, ACS Central Science, 8(1): 22-42 (2022).
  • Sztain, T., Ahn, S-H, Bogetti, AT, Casalino, LC, Goldsmith, JA, Seitz, E, McCool, RS, Kearns, FL, Acosta-Reyes, Fm Maji, S, Mashayekhi, G, Mccammon, JA, Ourmazd, A., Frank, J, McClellan JS, Chong, LT, Amaro, RE, “A glycan gate controls opening of the SARS-CoV-2 spike protein,” Nature Chemistry, 13 (10) 963-968 (2021).
  • Votapka, L.W., Jagger B.R., Heyneman A.L., and Amaro R.E., “SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding”, J. Phys. Chem. B. 121, 3597–3606 (2017). doi: 10.1021/acs.jpcb.6b09388.
  • Shi, K., Carpenter, M.A., Banerjee, S., Shaban, N.M., Kurahashi, K., Salamango, D.J., McCann, J.L., Starrett, G.J., Duffy, J.V., Demir, O., Amaro, R.E., Harki, D.A., Harris, R.S., Aihara, H., “Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B”, Nature Struct. Mol. Biol. 24,131–139 (2017). doi: 10.1038/nsmb.3344 (2016).
  • Malmstrom, R., Kornev, A., Taylor, S. and Amaro, R.E., “Allostery through the computational microscope: cAMP activation of a canonical signaling domain,” Nature Comm. 6, 7588 (2015). doi: 10.1038/ncomms8588.
  • Amaro, R.E., Swift, R.V., Votapka, L., Li, W.W., Walker, R.C., Bush, R.M., “Mechanism of 150-Cavity Formation in Influenza Neuraminidase”, Nature Comm. 2, 388 (2011). doi: 10.1038/ncomms1390
  • Amaro, R.E., Schnaufer, Interthal, H.A., Hol, W., Stuart, K., McCammon, J.A., “Discovery of the First Inhibitors of an Essential RNA Editing Ligase in Trypanosoma brucei”, Proc. Nat. Acad. Sci. USA 105, 17278 – 17283 (2008).
  • A. Dommer, L. Casalino, F. Kearns, M. Rosenfeld, N. Wauer, S.-H. Ahn, J. Russo, S. Oliveira, C. Morris, A. Bogetti, A. Trifan, A. Brace, T. Sztain, A. Clyde, H. Ma, C. Chennubhotla, H. Lee, M. Turilli, S. Khalid, T. Tamayo-Mendoza, M. Welborn, A. Christensen, D.G.A. Smith, Z. Qiao, S.K. Sirumalla, M. O’Connor, F. Manby, A. Anandkumar, D. Hardy, J. Phillips, A. Stern, J. Romero, D. Clark, M. Dorrell, T. Maiden, L. Huang, J. McCalpin, C. Woods, A. Gray, M. Williams, B. Barker, H. Rajapaksha, R. Pitts, T. Gibbs, J. Stone, D. Zuckerman, A. Mulholland, T. Miller, S. Jha, A. Ramanathan, L. Chong, R. Amaro, #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol, Journal of High Performance Computing Applications, 2022;0(0). doi:10.1177/10943420221128233
  • Lorenzo Casalino, Abigail Dommer, Zied Gaieb, Emilia P. Barros, Terra Sztain, Surl-Hee Ahn, Anda Trifan, Alexander Brace, Anthony Bogetti, Heng Ma, Hyungro Lee, Matteo Turilli, Syma Khalid, Lillian Chong, Carlos Simmerling, David J. Hardy, Julio D. C. Maia, James C. Phillips, Thorsten Kurth, Abraham Stern, Lei Huang, John McCalpin, Mahidhar Tatineni, Tom Gibbs, John E. Stone, Shantenu Jha, Arvind Ramanathan, Rommie E. Amaro; AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics. The International Journal of High Performance Computing Applications. April 2021. doi:10.1177/10943420211006452.


Rommie E. Amaro holds the Distinguished Professorship in Theoretical and Computational Chemistry at the University of California, San Diego. She grew up on the south side of Chicago and received her B.S. in Chemical Engineering (1999) and her Ph.D. in Chemistry (2005) from the University of Illinois at Urbana-Champaign. Rommie was a NIH postdoctoral fellow with Prof. J. Andrew McCammon at UC San Diego from 2005-2009, and started her independent lab at the University of California, Irvine in 2009. In 2011 she moved to UC San Diego. She is the recipient of an NIH New Innovator Award, the Presidential Early Career Award for Scientists and Engineers, the ACS COMP OpenEye Outstanding Junior Faculty Award, the ACS Kavli Foundation Emerging Leader in Chemistry, the Corwin Hansch Award, and the 2020 ACM Gordon Bell Special Prize for COVID19. Rommie’s scientific interests lie at the intersection of computer-aided drug discovery and biophysical simulation. Her scientific vision revolves around expanding the range and complexity of molecular constituents represented in atomic-level molecular dynamics simulations, the development of novel multiscale methods for elucidating their time dependent dynamics, and the discovery of novel chemical matter controlling biological function.