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Maria Nagan

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Maria Nagan

Stony Brook University

    1999 …2026

    Research activity per year

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    • Deciphering hydration patterns across RNA conformations: Insights into water-mediated RNA recognition

      Ghosh, A. P., DuVal, J. N., Cavoto, A. M. & Nagan, M. C., Jun 2026, In: Current Research in Structural Biology. 11, 100184.

      Stony Brook University

      Research output: Contribution to journal › Article › peer-review

      Open Access

    • Recent Developments in Amber Biomolecular Simulations

      Case, D. A., Cerutti, D. S., Cruzeiro, V. W. D., Darden, T. A., Duke, R. E., Ghazimirsaeed, M., Giambaşu, G. M., Giese, T. J., Götz, A. W., Harris, J. A., Kasavajhala, K., Lee, T. S., Li, Z., Lin, C., Liu, J., Miao, Y., Salomon-Ferrrer, R., Shen, J., Snyder, R. & Swails, J. & 11 others, Walker, R. C., Wang, J., Wu, X., Zeng, J., Cheatham, T. E., Roe, D. R., Roitberg, A., Simmerling, C., York, D. M., Nagan, M. C. & Merz, K. M., Aug 11 2025, In: Journal of Chemical Information and Modeling. 65, 15, p. 7835-7843 9 p.

      Stony Brook University

      Research output: Contribution to journal › Article › peer-review

      Open Access
      101 Scopus citations

    • Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment

      Linzer, J. T., Aminov, E., Abdullah, A. S., Kirkup, C. E., Diaz Ventura, R. I., Bijoor, V. R., Jung, J., Huang, S., Tse, C. G., Álvarez Toucet, E., Onghai, H. P., Ghosh, A. P., Grodzki, A. C., Haines, E. R., Iyer, A. S., Khalil, M. K., Leong, A. P., Neuhaus, M. A., Park, J. & Shahid, A. & 4 others, Xie, M., Ziembicki, J. M., Simmerling, C. & Nagan, M. C., Aug 12 2024, In: Journal of Chemical Information and Modeling. 64, 15, p. 6092-6104 13 p.

      Stony Brook University

      Research output: Contribution to journal › Article › peer-review

      Open Access
      3 Scopus citations

    • Adjusting the Energy Profile for CH-O Interactions Leads to Improved Stability of RNA Stem-Loop Structures in MD Simulations

      Raguette, L. E., Gunasekera, S. S., Diaz Ventura, R. I., Aminov, E., Linzer, J. T., Parwana, D., Wu, Q., Simmerling, C. & Nagan, M. C., Aug 22 2024, In: Journal of Physical Chemistry B. 128, 33, p. 7921-7933 13 p.

      Stony Brook University

      Research output: Contribution to journal › Article › peer-review

      Open Access
      7 Scopus citations

    • AmberTools

      Case, D. A., Aktulga, H. M., Belfon, K., Cerutti, D. S., Cisneros, G. A., Cruzeiro, V. W. D., Forouzesh, N., Giese, T. J., Götz, A. W., Gohlke, H., Izadi, S., Kasavajhala, K., Kaymak, M. C., King, E., Kurtzman, T., Lee, T. S., Li, P., Liu, J., Luchko, T. & Luo, R. & 27 others, Manathunga, M., Machado, M. R., Nguyen, H. M., O’Hearn, K. A., Onufriev, A. V., Pan, F., Pantano, S., Qi, R., Rahnamoun, A., Risheh, A., Schott-Verdugo, S., Shajan, A., Swails, J., Wang, J., Wei, H., Wu, X., Wu, Y., Zhang, S., Zhao, S., Zhu, Q., Cheatham, T. E., Roe, D. R., Roitberg, A., Simmerling, C., York, D. M., Nagan, M. C. & Merz, K. M., Oct 23 2023, In: Journal of Chemical Information and Modeling. 63, 20, p. 6183-6191 9 p.

      Stony Brook University

      Research output: Contribution to journal › Article › peer-review

      Open Access
      1660 Scopus citations
    View all 19 Research outputs