The GROMOS software for biomolecular simulation: GROMOS05. - Markus Christen; Philippe H. Hünenberger; Dirk Bakowies; Riccardo Baron; Roland Bürgi; Daan P. Geerke; Tim N. Heinz; Mika A. Kastenholz; Vincent Kräutler; Chris Oostenbrink; Christine Peter; Daniel Trzesniak; et al. (J. Comput. Chem., 2005)

Oxidative addition of the ethane C-C bond to Pd. An ab initio benchmark and DFT validation study. - G. Theodoor De Jong; Daan P. Geerke; Axel Diefenbach; Miquel Solà; Friedrich Matthias Bickelhaupt (J. Comput. Chem., 2005)

Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models. - Haibo Yu 003; Daan P. Geerke; Haiyan Liu; Wilfred F. van Gunsteren (J. Comput. Chem., 2006)

On the direct calculation of the free energy of quantization for molecular systems in the condensed phase. - Daan P. Geerke; Sandra Luber; Koni H. Marti; Wilfred F. van Gunsteren (J. Comput. Chem., 2009)

Charge Group Partitioning in Biomolecular Simulation. - Stefan Canzar; Mohammed El-Kebir; René Pool; Khaled M. Elbassioni; Alpeshkumar K. Malde; Alan E. Mark; Daan P. Geerke; Leen Stougie; Gunnar W. Klau (RECOMB, 2012)

New functionalities in the GROMOS biomolecular simulation software. - Anna-Pitschna E. Kunz; Jane R. Allison; Daan P. Geerke; Bruno A. C. Horta; Philippe H. Hünenberger; Sereina Riniker; Nathan Schmid; Wilfred F. van Gunsteren (J. Comput. Chem., 2012)

Free Energy Calculations Give Insight into the Stereoselective Hydroxylation of α-Ionones by Engineered Cytochrome P450 BM3 Mutants. - Stephanie B. A. De Beer; Harini Venkataraman; Daan P. Geerke; Chris Oostenbrink; Nico P. E. Vermeulen (J. Chem. Inf. Model., 2012)

Charge Group Partitioning in Biomolecular Simulation. - Stefan Canzar; Mohammed El-Kebir; René Pool; Khaled M. Elbassioni; Alan E. Mark; Daan P. Geerke; Leen Stougie; Gunnar W. Klau (J. Comput. Biol., 2013)

A systematic approach to calibrate a transferable polarizable force field parameter set for primary alcohols. - Koen Visscher; C. Ruben Vosmeer; Rosa A. Luirink; Daan P. Geerke (J. Comput. Chem., 2017)

eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations. - Luigi Capoferri; Marc van Dijk; Ariën S. Rustenburg; Tsjerk A. Wassenaar; Derk P. Kooi; Eko Aditya Rifai; Nico P. E. Vermeulen; Daan P. Geerke (J. Cheminformatics, 2017)

Comprehensive and Automated Linear Interaction Energy Based Binding-Affinity Prediction for Multifarious Cytochrome P450 Aromatase Inhibitors. - Marc van Dijk; Antonius ter Laak; Jörg D. Wichard; Luigi Capoferri; Nico P. E. Vermeulen; Daan P. Geerke (J. Chem. Inf. Model., 2017)

Multiple-Choice Knapsack for Assigning Partial Atomic Charges in Drug-Like Molecules. - Martin S. Engler; Bertrand Caron; Lourens E. Veen; Daan P. Geerke; Alan E. Mark; Gunnar W. Klau (WABI, 2018)

Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2. - Eko Aditya Rifai; Marc van Dijk; Nico P. E. Vermeulen; Daan P. Geerke (J. Comput. Aided Mol. Des., 2018)

Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approach. - Martin S. Engler; Bertrand Caron; Lourens E. Veen; Daan P. Geerke; Alan E. Mark; Gunnar W. Klau (Algorithms Mol. Biol., 2019)

A Comparative Linear Interaction Energy and MM/PBSA Study on SIRT1-Ligand Binding Free Energy Calculation. - Eko Aditya Rifai; Marc van Dijk; Nico P. E. Vermeulen; Arry Yanuar; Daan P. Geerke (J. Chem. Inf. Model., 2019)

OFraMP: a fragment-based tool to facilitate the parametrization of large molecules. - Martin Stroet; Bertrand Caron; Martin S. Engler; Jimi van der Woning; Aude Kauffmann; Marc van Dijk; Mohammed El-Kebir; Koen Visscher; Josef Holownia; Callum Macfarlane; Brian J. Bennion; Svetlana Gelpi-Dominguez; et al. (J. Comput. Aided Mol. Des., 2023)

Computational Strategies for Broad Spectrum Venom Phospholipase A2 Inhibitors. - David A. Poole; Laura-Oana Albulescu; Jeroen Kool; Nicholas R. Casewell; Daan P. Geerke (J. Chem. Inf. Model., 2025)