| MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues C Kaya, A Armutlulu, S Ekesan, T Haliloglu Nucleic acids research 41 (W1), W249-W255, 2013 | 76 | 2013 |
| Development of range-corrected deep learning potentials for fast, accurate quantum mechanical/molecular mechanical simulations of chemical reactions in solution J Zeng, TJ Giese, S Ekesan, DM York Journal of chemical theory and computation 17 (11), 6993-7009, 2021 | 53 | 2021 |
| An ontology for facilitating discussion of catalytic strategies of RNA-cleaving enzymes PC Bevilacqua, ME Harris, JA Piccirilli, C Gaines, A Ganguly, ... ACS chemical biology 14 (6), 1068-1076, 2019 | 53 | 2019 |
| Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8–17 DNAzyme in solution Ş Ekesan, DM York Nucleic acids research 47 (19), 10282-10295, 2019 | 30 | 2019 |
| Combined QM/MM, machine learning path integral approach to compute free energy profiles and kinetic isotope effects in RNA cleavage reactions TJ Giese, J Zeng, S Ekesan, DM York Journal of chemical theory and computation 18 (7), 4304-4317, 2022 | 19 | 2022 |
| Transferable pseudoclassical electrons for aufbau of atomic ions S Ekesan, S Kale, J Herzfeld Journal of computational chemistry 35 (15), 1159-1164, 2014 | 18 | 2014 |
| Extension of the variational free energy profile and multistate Bennett acceptance ratio methods for high-dimensional potential of mean force profile analysis TJ Giese, S Ekesan, DM York The Journal of Physical Chemistry A 125 (19), 4216-4232, 2021 | 16 | 2021 |
| Pointillist rendering of electron charge and spin density suffices to replicate trends in atomic properties S Ekesan, J Herzfeld Proceedings of the Royal Society A: Mathematical, Physical and Engineering …, 2015 | 12 | 2015 |
| RNA electrostatics: how ribozymes engineer active sites to enable catalysis S Ekesan, E McCarthy, DA Case, DM York The Journal of Physical Chemistry B 126 (32), 5982-5990, 2022 | 9 | 2022 |
| Exchange potentials for semi-classical electrons J Herzfeld, S Ekesan Physical Chemistry Chemical Physics 18 (44), 30748-30753, 2016 | 9 | 2016 |
| Magnetism and Bond Order in Diatomic Molecules Described by Semiclassical Electrons S Ekesan, DY Lin, J Herzfeld The Journal of Physical Chemistry B 120 (26), 6264-6269, 2016 | 8 | 2016 |
| Framework for conducting and analyzing crystal simulations of nucleic acids to aid in modern force field evaluation S Ekesan, DM York The Journal of Physical Chemistry B 123 (22), 4611-4624, 2019 | 6 | 2019 |
| Dissociative transition state in hepatitis delta virus ribozyme catalysis B Weissman, S Ekesan, HC Lin, S Gardezi, NS Li, TJ Giese, E McCarthy, ... Journal of the American Chemical Society 145 (5), 2830-2839, 2023 | 4 | 2023 |
| Who stole the proton? Suspect general base guanine found with a smoking gun in the pistol ribozyme Ş Ekesan, DM York Organic & biomolecular chemistry 20 (31), 6219-6230, 2022 | 4 | 2022 |
| Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology E McCarthy, Ş Ekesan, TJ Giese, TJ Wilson, J Deng, L Huang, DMJ Lilley, ... Nucleic acids research 51 (9), 4508-4518, 2023 | 3 | 2023 |
| Surface-Accelerated String Method for Locating Minimum Free Energy Paths TJ Giese, S Ekesan, E McCarthy, Y Tao, DM York Journal of Chemical Theory and Computation, 2024 | | 2024 |
| DNA can do it! Catalytic mechanism of the 8-17 DNAzyme S Ekesan, D York ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 258, 2019 | | 2019 |
| RNA-cleavage by DNA and RNA enzymes S Ekesan, D York ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 258, 2019 | | 2019 |
| Simulating nucleic acids in their crystal environment: A test for gauging accuracy of modern force fields S Ekesan, D York ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 255, 2018 | | 2018 |
| Multiple contributions to the exchange potential for semi-classical electrons J Herzfeld, S Ekesan ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 252, 2016 | | 2016 |
