The Maximum Entropy Production Principle and Linear Irreversible Processes. - Pasko Zupanovic; Domagoj Kuic; Zeljana Bonacic Losic; Drazen Petrov; Davor Juretic; Milan Brumen (Entropy, 2010)

Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications. - Christian Margreitter; Drazen Petrov; Bojan Zagrovic (Nucleic Acids Res., 2013)

A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications. - Drazen Petrov; Christian Margreitter; Melanie Grandits; Chris Oostenbrink; Bojan Zagrovic (PLoS Comput. Biol., 2013)

Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments? - Drazen Petrov; Bojan Zagrovic (PLoS Comput. Biol., 2014)

Correcting electrostatic artifacts due to net-charge changes in the calculation of ligand binding free energies. - Christoph Öhlknecht; Bettina Lier; Drazen Petrov; Julian Fuchs; Chris Oostenbrink (J. Comput. Chem., 2020)

Toward Automated Free Energy Calculation with Accelerated Enveloping Distribution Sampling (A-EDS). - Jan Walther Perthold; Drazen Petrov; Chris Oostenbrink (J. Chem. Inf. Model., 2020)

Perturbation Free-Energy Toolkit: An Automated Alchemical Topology Builder. - Drazen Petrov (J. Chem. Inf. Model., 2021)