Molecular dynamics to enhance structure-based virtual screening on cathepsin B. - Mitja Ogrizek; Samo Turk; Samo Lesnik; Izidor Sosic; Milan Hodoscek; Bojana Mirkovic; Janko Kos; Dusanka Janezic; Stanislav Gobec; Janez Konc (J. Comput. Aided Mol. Des., 2015)

Modeling enzyme-ligand binding in drug discovery. - Janez Konc; Samo Lesnik; Dusanka Janezic (J. Cheminformatics, 2015)

ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites. - Janez Konc; Benjamin T. Miller; Tanja Stular; Samo Lesnik; H. Lee Woodcock III; Bernard R. Brooks; Dusanka Janezic (J. Chem. Inf. Model., 2015)

LiSiCA: A Software for Ligand-Based Virtual Screening and Its Application for the Discovery of Butyrylcholinesterase Inhibitors. - Samo Lesnik; Tanja Stular; Boris Brus; Damijan Knez; Stanislav Gobec; Dusanka Janezic; Janez Konc (J. Chem. Inf. Model., 2015)

Ligand-based virtual screening interface between PyMOL and LiSiCA. - Athira Dilip; Samo Lesnik; Tanja Stular; Dusanka Janezic; Janez Konc (J. Cheminformatics, 2016)

BoBER: web interface to the base of bioisosterically exchangeable replacements. - Samo Lesnik; Blaz Skrlj; Nika Erzen; Urban Bren; Stanislav Gobec; Janez Konc; Dusanka Janezic (J. Cheminformatics, 2017)

Discovery of Novel Potential Human Targets of Resveratrol by Inverse Molecular Docking. - Katarina Kores; Samo Lesnik; Urban Bren; Dusanka Janezic; Janez Konc (J. Chem. Inf. Model., 2019)

Potential Energy Function for Fentanyl-Based Opioid Pain Killers. - Samo Lesnik; Milan Hodoscek; Urban Bren; Christoph Stein; Ana-Nicoleta Bondar (J. Chem. Inf. Model., 2020)

Loop Grafting between Similar Local Environments for Fc-Silent Antibodies. - Samo Lesnik; Milan Hodoscek; Barbara Podobnik; Janez Konc (J. Chem. Inf. Model., 2020)

CHARMM Force-Field Parameters for Morphine, Heroin, and Oliceridine, and Conformational Dynamics of Opioid Drugs. - Thomas Giannos; Samo Lesnik; Urban Bren; Milan Hodoscek; Tatiana Domratcheva; Ana-Nicoleta Bondar (J. Chem. Inf. Model., 2021)

ProBiS-Dock Database: A Web Server and Interactive Web Repository of Small Ligand-Protein Binding Sites for Drug Design. - Janez Konc; Samo Lesnik; Blaz Skrlj; Dusanka Janezic (J. Chem. Inf. Model., 2021)

ProBiS-Dock: A Hybrid Multitemplate Homology Flexible Docking Algorithm Enabled by Protein Binding Site Comparison. - Janez Konc; Samo Lesnik; Blaz Skrlj; Matej Sova; Matic Proj; Damijan Knez; Stanislav Gobec; Dusanka Janezic (J. Chem. Inf. Model., 2022)

Fentanyl and the Fluorinated Fentanyl Derivative NFEPP Elicit Distinct Hydrogen-Bond Dynamics of the Opioid Receptor. - Samo Lesnik; Urban Bren; Tatiana Domratcheva; Ana-Nicoleta Bondar (J. Chem. Inf. Model., 2023)

Unveiling polyphenol-protein interactions: a comprehensive computational analysis. - Samo Lesnik; Marko Jukic; Urban Bren (J. Cheminformatics, 2025)