MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues. - Cihan Kaya; Andac Armutlulu; Sölen Ekesan; Turkan Haliloglu (Nucleic Acids Res., 2013)

Transferable pseudoclassical electrons for aufbau of atomic ions. - Sölen Ekesan; Seyit Kale; Judith Herzfeld (J. Comput. Chem., 2014)

FE-ToolKit: A Versatile Software Suite for Analysis of High-Dimensional Free Energy Surfaces and Alchemical Free Energy Networks. - Timothy J. Giese; Ryan Snyder; Zeke Piskulich; German P. Barletta; Shi Zhang; Erika McCarthy; Sölen Ekesan; Darrin M. York (J. Chem. Inf. Model., 2025)