Daan P. Geerke

17 papers B 1C 1Journal 15
YearRankTypeTitle / Venue / Authors
2025 J jnl
Computational Strategies for Broad Spectrum Venom Phospholipase A
J. Chem. Inf. Model.
David A. Poole, Laura-Oana Albulescu, Jeroen Kool, Nicholas R. Casewell, Daan P. Geerke
2023 J jnl
OFraMP: a fragment-based tool to facilitate the parametrization of large molecules.
J. Comput. Aided Mol. Des.
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, Felice C. Lightstone, Tijs van der Storm, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau
2019 J jnl
A Comparative Linear Interaction Energy and MM/PBSA Study on SIRT1-Ligand Binding Free Energy Calculation.
J. Chem. Inf. Model.
Eko Aditya Rifai, Marc van Dijk, Nico P. E. Vermeulen, Arry Yanuar, Daan P. Geerke
2019 J jnl
Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approach.
Algorithms Mol. Biol.
Martin S. Engler, Bertrand Caron, Lourens E. Veen, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau
2018 J jnl
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.
J. Comput. Aided Mol. Des.
Eko Aditya Rifai, Marc van Dijk, Nico P. E. Vermeulen, Daan P. Geerke
2018 C conf
Multiple-Choice Knapsack for Assigning Partial Atomic Charges in Drug-Like Molecules.
WABI
Martin S. Engler, Bertrand Caron, Lourens E. Veen, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau
2017 J jnl
A systematic approach to calibrate a transferable polarizable force field parameter set for primary alcohols.
J. Comput. Chem.
Koen Visscher, C. Ruben Vosmeer, Rosa A. Luirink, Daan P. Geerke
2017 J jnl
Comprehensive and Automated Linear Interaction Energy Based Binding-Affinity Prediction for Multifarious Cytochrome P450 Aromatase Inhibitors.
J. Chem. Inf. Model.
Marc van Dijk, Antonius ter Laak, Jörg D. Wichard, Luigi Capoferri, Nico P. E. Vermeulen, Daan P. Geerke
2017 J jnl
eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations.
J. Cheminformatics
Luigi Capoferri, Marc van Dijk, Ariën S. Rustenburg, Tsjerk A. Wassenaar, Derk P. Kooi, Eko Aditya Rifai, Nico P. E. Vermeulen, Daan P. Geerke
2013 J jnl
Charge Group Partitioning in Biomolecular Simulation.
J. Comput. Biol.
Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled M. Elbassioni, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau
2012 B conf
Charge Group Partitioning in Biomolecular Simulation.
RECOMB
Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled M. Elbassioni, Alpeshkumar K. Malde, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau
2012 J jnl
Free Energy Calculations Give Insight into the Stereoselective Hydroxylation of α-Ionones by Engineered Cytochrome P450 BM3 Mutants.
J. Chem. Inf. Model.
Stephanie B. A. De Beer, Harini Venkataraman, Daan P. Geerke, Chris Oostenbrink, Nico P. E. Vermeulen
2012 J jnl
New functionalities in the GROMOS biomolecular simulation software.
J. Comput. Chem.
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
2009 J jnl
On the direct calculation of the free energy of quantization for molecular systems in the condensed phase.
J. Comput. Chem.
Daan P. Geerke, Sandra Luber, Koni H. Marti, Wilfred F. van Gunsteren
2006 J jnl
Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models.
J. Comput. Chem.
Haibo Yu, Daan P. Geerke, Haiyan Liu, Wilfred F. van Gunsteren
2005 J jnl
Oxidative addition of the ethane C-C bond to Pd. An
J. Comput. Chem.
G. Theodoor De Jong, Daan P. Geerke, Axel Diefenbach, Miquel Solà, Friedrich Matthias Bickelhaupt
2005 J jnl
The GROMOS software for biomolecular simulation: GROMOS05.
J. Comput. Chem.
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, Wilfred F. van Gunsteren