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Maria C. Nagan, Professor of Practice

Associate Dean for Curriculum, College of Arts and Sciences



B.S. 1997, Grinnell College (Grinnell, IA)
Ph.D. 2001, University of Minnesota – Twin Cities

435 Chemistry, 631-632-5793




The Nagan lab employs computational methods to understand how chemical functional groups affect RNA  structure and recognition. 

Visit The Nagan Group Website


Chemistry REU Site (PI) - supported by NSF CHE-2050541

Velay Program (PI) - supported by the Panaphil Foundation

SUNY SOAR (co-PI) - supported by the SUNY Chancellor

REsearch Leadership

Amber Molecular Dynamics Software  Executive Committee


ACS COMP Co-chair Programming, Mercury Executive Committee


Godfrey Excellence in Teaching Award, Fellow of the American Chemical Society, McNair Mentor Hall of Fame, Walker and Doris Allen Fellowship for Faculty Excellence


1. Hasan Metin Aktulga, Kellon Belfon, David S. Cerutti,Gerardo Andrés Cisneros, Vinícius Wilian D. Cruzeiro, Negin Forouzesh, Timothy J. Giese, Andreas W. Goëtz, Holger Gohlke, Saeed Izadi, Koushik Kasavajhala Mehmet C. Kaymak, Edward King, Tom Kurtzman, Tai-Sung Lee, Pengfei Li, Jian Liu, Tyler Luchko, Ray Luo, Madushanka Manathunga, Matias R. Machado, Hai Minh Nguyen, Kurt A. O’Hearn, Alexey Onufriev, Feng Pan, Sergio Pantano,Ruxi Qi, Ali Rahnamoun, Ali Risheh, Stephan Schott-Verdugo, Akhil Shajan,s Jason Swails, Junmei Wang, Haixin Wei, Xiongwu Wu, Yongxian Wu, Shi Zhang, Shiji Zhao,Qiang Zhu, Daniel R. Roe, , Darrin M. York, David A Case, Thomas E. Cheatham, III, Adrian Roitberg,C.L. Simmerling, Maria C. Nagan* and Kenneth M. Merz, Jr.*, AmberTools23, J. Chem. Inf. Model, 2023,

2. 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(24), 6316-6322.
3. Maddula, V., Rotenberg, S. A. and Nagan, M.C. “Computational Studies of the α/ß-Tubulin Heterodimeric Interface in Microtubules: The Impact of Phosphorylation of Ser165 in α-Tubulin” Biochemistry, 2022, 61(14), 1508-1516. Supplemental Cover. 
4. Nagan, M.C. “Using a Lab Wiki for Longevity and Knowledge Transfer in Undergraduate Research” International Journal of Quantum Chemistry, 2020,120 (20), e26262.
5. 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.
6. 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.
7. 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.
8. 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.