CHARMM: The biomolecular simulation program. - Bernard R. Brooks; Charles L. Brooks III; Alexander D. MacKerell Jr.; Lennart Nilsson; Robert J. Petrella; Benoît Roux; Y. Won; G. Archontis; Christian Bartels; Stefan Boresch; Amedeo Caflisch; Leo S. D. Caves; et al. (J. Comput. Chem., 2009)

Unorthodox uses of Bennett's acceptance ratio method. - Gerhard König; Stefan Bruckner; Stefan Boresch (J. Comput. Chem., 2009)

Avoiding the van der Waals endpoint problem using serial atomic insertion. - Stefan Boresch; Stefan Bruckner (J. Comput. Chem., 2011)

Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method. - Stefan Bruckner; Stefan Boresch (J. Comput. Chem., 2011)

Efficiency of alchemical free energy simulations. II. Improvements for thermodynamic integration. - Stefan Bruckner; Stefan Boresch (J. Comput. Chem., 2011)

Non-Boltzmann sampling and Bennett's acceptance ratio method: How to profit from bending the rules. - Gerhard König; Stefan Boresch (J. Comput. Chem., 2011)

Comparison of thermodynamic integration and Bennett's acceptance ratio for calculating relative protein-ligand binding free energies. - Anita de Ruiter; Stefan Boresch; Chris Oostenbrink (J. Comput. Chem., 2013)

Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial. - Benjamin T. Miller; Rishi P. Singh; Vinushka Schalk; Yuri Pevzner; Jingjun Sun; Carrie S. Miller; Stefan Boresch; Toshiko Ichiye; Bernard R. Brooks; H. Lee Woodcock III (PLoS Comput. Biol., 2014)

Computing converged free energy differences between levels of theory via nonequilibrium work methods: Challenges and opportunities. - Fiona L. Kearns; Phillip S. Hudson; Henry L. Woodcock; Stefan Boresch (J. Comput. Chem., 2017)

Common Hits Approach: Combining Pharmacophore Modeling and Molecular Dynamics Simulations. - Marcus Wieder; Arthur Garon; Ugo Perricone; Stefan Boresch; Thomas Seidel; Anna Maria Almerico; Thierry Langer (J. Chem. Inf. Model., 2017)

SAR-Guided Scoring Function and Mutational Validation Reveal the Binding Mode of CGS-8216 at the α1+/γ2- Benzodiazepine Site. - David C. B. Siebert; Marcus Wieder; Lydia Schlener; Petra Scholze; Stefan Boresch; Thierry Langer; Michael Schnürch; Marko D. Mihovilovic; Lars Richter; Margot Ernst; Gerhard F. Ecker (J. Chem. Inf. Model., 2018)

Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program. - Marcus Wieder; Markus Fleck; Benedict Braunsfeld; Stefan Boresch (J. Comput. Chem., 2022)

On Analytical Corrections for Restraints in Absolute Binding Free Energy Calculations. - Stefan Boresch (J. Chem. Inf. Model., 2024)