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Kirmizialtin, Serdal, Kenneth A. Johnson, and Ron Elber. "Enzyme selectivity of HIV reverse transcriptase: conformations, ligands, and free energy partition." The Journal of Physical Chemistry B 119, no. 35 (2015): 11513-11526.
Kirmizialtin, Serdal, Scott P. Hennelly, Alexander Schug, Jose N. Onuchic, and Karissa Y. Sanbonmatsu. "Chapter Nine-Integrating Molecular Dynamics Simulations with Chemical Probing Experiments Using SHAPE-FIT." Methods in enzymology 553 (2015): 215-234.
Kirmizialtin, Serdal, Virginia Nguyen, Kenneth A. Johnson, and Ron Elber. "How conformational dynamics of DNA polymerase select correct substrates: experiments and simulations." Structure 20, no. 4 (2012): 618-627.
Kirmizialtin, Serdal, Suzette A. Pabit, Steve P. Meisburger, Lois Pollack, and Ron Elber. "RNA and its ionic cloud: solution scattering experiments and atomically detailed simulations." Biophysical journal 102, no. 4 (2012): 819-828.
Kirmizialtin, Serdal, and Ron Elber. "Revisiting and computing reaction coordinates with Directional Milestoning." The journal of physical chemistry A 115, no. 23 (2011): 6137-6148.