Computational analysis of local membrane properties. - Vytautas Gapsys; Bert L. de Groot; Rodolfo Briones (J. Comput. Aided Mol. Des., 2013)

pmx: Automated protein structure and topology generation for alchemical perturbations. - Vytautas Gapsys; Servaas Michielssens; Daniel Seeliger; Bert L. de Groot (J. Comput. Chem., 2015)

pmx Webserver: A User Friendly Interface for Alchemistry. - Vytautas Gapsys; Bert L. de Groot (J. Chem. Inf. Model., 2017)

Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset. - Eddy Elisée; Vytautas Gapsys; Nawel Mele; Ludovic Chaput; Edithe Selwa; Bert L. de Groot; Bogdan I. Iorga (J. Comput. Aided Mol. Des., 2019)

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. - Andrea Rizzi; Travis Jensen; David R. Slochower; Matteo Aldeghi; Vytautas Gapsys; Dimitris Ntekoumes; Stefano Bosisio; Michail Papadourakis; Niel M. Henriksen; Bert L. de Groot; Zoe Cournia; Alex Dickson; et al. (J. Comput. Aided Mol. Des., 2020)

Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software. - Yuriy Khalak; Gary Tresadern; Bert L. de Groot; Vytautas Gapsys (J. Comput. Aided Mol. Des., 2021)

Pre-Exascale Computing of Protein-Ligand Binding Free Energies with Open Source Software for Drug Design. - Vytautas Gapsys; David F. Hahn; Gary Tresadern; David L. Mobley; Markus Rampp; Bert L. de Groot (J. Chem. Inf. Model., 2022)

GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design. - Carsten Kutzner; Christian Kniep; Austin Cherian; Ludvig Nordstrom; Helmut Grubmüller; Bert L. de Groot; Vytautas Gapsys (J. Chem. Inf. Model., 2022)

Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions. - David F. Hahn; Vytautas Gapsys; Bert L. de Groot; David L. Mobley; Gary Tresadern (J. Chem. Inf. Model., 2024)

Resolving coupled pH titrations using alchemical free energy calculations. - Carter J. Wilson; Bert L. de Groot; Vytautas Gapsys (J. Comput. Chem., 2024)

Quantification of the Impact of Structure Quality on Predicted Binding Free Energy Accuracy. - Sudarshan Behera; David F. Hahn; Carter J. Wilson; Simone Marsili; Gary Tresadern; Vytautas Gapsys; Bert L. de Groot (J. Chem. Inf. Model., 2025)