ProtSqueeze: Simple and Effective Automated Tool for Setting up Membrane Protein Simulations. - Semen O. Yesylevskyy (J. Chem. Inf. Model., 2007)

Polarizable Water Model for the Coarse-Grained MARTINI Force Field. - Semen O. Yesylevskyy; Lars V. Schäfer; Durba Sengupta; Siewert J. Marrink (PLoS Comput. Biol., 2010)

Integrated tools for molecular dynamics simulation data analysis in the MolDynGrid virtual laboratory. - Oleksandr V. Savytskyi; Ievgen A. Sliusar; Semen O. Yesylevskyy; Sergii G. Stirenko; Alexander I. Kornelyuk (IDAACS (1), 2011)

Pteros: Fast and easy to use open-source C++ library for molecular analysis. - Semen O. Yesylevskyy (J. Comput. Chem., 2012)

Pteros 2.0: Evolution of the fast parallel molecular analysis library for C++ and python. - Semen O. Yesylevskyy (J. Comput. Chem., 2015)

Selective Inhibition of STAT3 with Respect to STAT1: Insights from Molecular Dynamics and Ensemble Docking Simulations. - Semen O. Yesylevskyy; Christophe Ramseyer; Marc Pudlo; Jean-René Pallandre; Christophe Borg (J. Chem. Inf. Model., 2016)

Flexoelectric and Piezoelectric Coupling in a Bended MoS2 Monolayer. - Hanna V. Shevliakova; Semen O. Yesylevskyy; Ihor Kupchak; Galina I. Dovbeshko; Yunseok Kim; Anna N. Morozovska (Symmetry, 2021)

MolAR: Memory-Safe Library for Analysis of MD Simulations Written in Rust. - Semen O. Yesylevskyy (J. Comput. Chem., 2025)