Dynamic channels in biomolecular systems: Path analysis and visualization. - Norbert Lindow; Daniel Baum; Ana-Nicoleta Bondar; Hans-Christian Hege (BioVis, 2012)

Exploring cavity dynamics in biomolecular systems. - Norbert Lindow; Daniel Baum; Ana-Nicoleta Bondar; Hans-Christian Hege (BMC Bioinform., 2013)

Revised CHARMM force field parameters for iron-containing cofactors of photosystem II. - Suliman Adam; Michaela Knapp-Mohammady; Jun Yi; Ana-Nicoleta Bondar (J. Comput. Chem., 2018)

Using Graphs of Dynamic Hydrogen-Bond Networks To Dissect Conformational Coupling in a Protein Motor. - Konstantina Karathanou; Ana-Nicoleta Bondar (J. Chem. Inf. Model., 2019)

Cover Image. - Oskar Klaja; James A. Frank; Dirk Trauner; Ana-Nicoleta Bondar (J. Comput. Chem., 2020)

Potential energy function for a photo-switchable lipid molecule. - Oskar Klaja; James A. Frank; Dirk Trauner; Ana-Nicoleta Bondar (J. Comput. Chem., 2020)

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)

C-Graphs Tool with Graphical User Interface to Dissect Conserved Hydrogen-Bond Networks: Applications to Visual Rhodopsins. - Éva Bertalan; Elena Lesca; Gebhard F. X. Schertler; Ana-Nicoleta Bondar (J. Chem. Inf. Model., 2021)

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)

Interactive Interface for Graph-Based Analyses of Dynamic H-Bond Networks: Application to Spike Protein S. - Malte Siemers; Ana-Nicoleta Bondar (J. Chem. Inf. Model., 2021)

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)