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1. Ghosh, A.P., DuVal, J.N., Cavoto, A.M. and Nagan*, M.C. Deciphering hydration patterns
across RNA conformations: Insights into water-mediated RNA recognition. Current Research
in Structural Biology 2026,11, 100184, doi.org/10.1016/j.crstbi.2026.100184.
2. D.A. Case, D.S. Cerutti, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, M. Ghazimirsaeed,
G.M. Giambasu, T.J. Giese, A.W. Götz, J.A. Harris, K. Kasavajhala, T. Lee, Z. Li,
C. Lin, J. Liu, Y. Miao, R. Salomon-Ferrrer, J. Shen, R. Snyder, J. Swails, R.C. Walker,
J. Wang, X. Wu, J. Zeng, T.E. Cheatham, III, D.R. Roe, A. Roitberg, C. Simmerling,
D.M. York, M.C. Nagan*, K.M. Merz*, Jr. Recent Developments in Amber Biomolecular
Simulations. J. Chem. Inf. Model. 2025, 65, 7835-7843, doi.org/10.1021/acs.jcim.5c01063.
3. Raguette, L.E., Gunasekera, S.S., Ventura Diaz, R.I., Aminov, E., Linzer, J.T., Parwana, D., Wu, Q., Simmerling, C. and Nagan*, M.C. “Adjusting the energy profile
for CH–O interactions leads to improved stability of RNA stem-loop structures in MD
simulations” J. Phys. Chem. B, 2024, 128, 7921-7933, doi.org/10.1021/acs.jpcb.4c01910.
4. Linzer, J.T., Aminov, E.,Abdullah, A.S., Kirkup, C., Bijoor, V. R.Chong, J., Ventura Diaz, R.I., Grodzki, A.C., Haines, E.R.,Huang, S.Iyer, A.S., Khalil, M.K., Leong, A. P.Neuhaus, M. A., Onghai, H.P., Park, J., Tse, C.G., Álvarez Toucet, E.,Xie, M., Ziembicki, J. M., Simmerling, C. and Nagan*, M.C. “Accurately Folding RNA Stem-Loops in Implicit Solvent”
J. Chem. Inf. Model, 2024, 64, 6092-6104, doi.org/10.1021/acs.jcim.4c00756.
5. D. A. Case; H. M. Aktulga; K. Belfon; D. S. Cerutti; G. A. Cisneros; V. W. D. Cruzeiro;
N. Forouzesh; T. J. Giese; A. W. Götz; H. Gohlke; S. Izadi; K. Kasavajhala; M. C.
Kaymak; E. King; T. Kurtzman; T.-S. Lee; P. Li; J. Liu; T. Luchko; R. Luo; M. Manathunga;
M. R. Machado; H. M. Nguyen; K. A. O’Hearn; A. V. Onufriev; F. Pan; S. Pantano; R.
Qi; A. Rahnamoun; A. Risheh; S. Schott-Verdugo; A. Shajan; J. Swails; J. Wang; H.
Wei; X. Wu; Y. Wu; S. Zhang; S. Zhao; Q. Zhu; T. E. Cheatham, III; D. R. Roe; A. Roitberg;
C. Simmerling; D. M. York; Nagan*, M.C. and Merz, K.M. Jr.*, AmberTools23, J. Chem. Inf. Model, 2023, 63, 6183-6191, doi.org/10.1021/acs.jcim.3c01153.
6. Anderson, K., Arradondo, S., Ball, K.A., Bruce, C., Gomez, M.A., He, K., Hendrickson,
H., Madison, L., Ringer McDonald, A., Nagan, M.C., Scott, C.E., Soto, P., Tomlinson,
A., Varner, M. and Parish*, C. “The Impacts of the Molecular Education and Research
Consortium in Undergraduate Computational Chemistry on the Careers of Women in Computational
Chemistry” J. Chem. Inf. Model, 2022,62, 6316-6322, doi.org/10.1021/acs.jcim.2c00566.
7. Maddula, V., Holtzman, N. S., Nagan*, M.C. and Rotenberg*, S. A. “Computational Studies of the
α/ß-Tubulin Heterodimeric Interface in Microtubules: The Impact of Phosphorylation
of Ser165 in α-Tubulin” Biochemistry, 2022, 61, 1508-1516. Cover. doi.org/10.1021/acs.biochem.2c00154.
8. Nagan*, M.C. “Using a Lab Wiki for Longevity and Knowledge Transfer in Undergraduate
Research” International Journal of Quantum Chemistry, 2020,120, e26262. doi.org/10.1002/qua.26262.
9. Palermo, G.; Armacost, K.A. and Nagan, M.C. “Women Make COMP: Mentoring the Next
Generation of Women in Computational Chemistry” J. Chem. Inf. Model, 2019, 59, 4061-4062, doi.org/10.1021/acs.jcim.9b00643.
10. Witts, R.N.;Hopson, E.C.; Koballa, D.E.; Van Boening, T.A.; Hopkins, N.H.; Patterson, E.V. and Nagan, M.C. “Backbone-Base Interactions Critical to Quantum
Stabilization of Transfer RNA Anticodon Structure” J. Phys. Chem. B, 2013, 117, 7489-7497, doi.org/10.1021/jp400084p.
11. Michael, L.A.; Chenault, J.A.; Miller III, B.R.; Knolhoff, A.M. and Nagan, M.C. “Water, Shape-Recognition, Salt Bridges and Pi-Cation Interactions
Differentiate Peptide Recognition of the HIV Rev-Responsive Element” J. Mol. Biol. 2009, 392, 774-786, doi.org/10.1016/j.jmb.2009.07.047.
12. McCrate, N.E.; Varner, M.E.; Kim, K.I. and Nagan, M.C. “Molecular Dynamics Simulations of Human tRNALys,3UUU: The Role of Modified Bases in mRNA Recognition” Nucleic Acids Res. 2006, 34, 5361-5368, doi.org/10.1093/nar/gkl580.
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