Daan P. Geerke

Publication Activity (10 Years)

Years Active: 2005-2023
Publications (10 Years): 8

Top Topics

Chemical Reactions

Top Venues

J. Chem. Inf. Model.

J. Comput. Aided Mol. Des.

J. Comput. Biol.

J. Comput. Chem.

Publications

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
OFraMP: a fragment-based tool to facilitate the parametrization of large molecules. J. Comput. Aided Mol. Des. 37 (8) (2023)
Martin S. Engler, Bertrand Caron, Lourens Veen, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau
Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approach. Algorithms Mol. Biol. 14 (1) (2019)
Eko Aditya Rifai, Marc van Dijk, Nico P. E. Vermeulen, Arry Yanuar, Daan P. Geerke
A Comparative Linear Interaction Energy and MM/PBSA Study on SIRT1-Ligand Binding Free Energy Calculation. J. Chem. Inf. Model. 59 (9) (2019)
Martin S. Engler, Bertrand Caron, Lourens Veen, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau
Multiple-Choice Knapsack for Assigning Partial Atomic Charges in Drug-Like Molecules. WABI (2018)
Eko Aditya Rifai, Marc van Dijk, Nico P. E. Vermeulen, Daan P. Geerke
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. 32 (1) (2018)
Marc van Dijk, Antonius ter Laak, Jörg D. Wichard, Luigi Capoferri, Nico P. E. Vermeulen, Daan P. Geerke
Comprehensive and Automated Linear Interaction Energy Based Binding-Affinity Prediction for Multifarious Cytochrome P450 Aromatase Inhibitors. J. Chem. Inf. Model. 57 (9) (2017)
Luigi Capoferri, Marc van Dijk, Ariën S. Rustenburg, Tsjerk A. Wassenaar, Derk P. Kooi, Eko Aditya Rifai, Nico P. E. Vermeulen, Daan P. Geerke
eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations. J. Cheminformatics 9 (1) (2017)
Koen Visscher, C. Ruben Vosmeer, Rosa A. Luirink, Daan P. Geerke
A systematic approach to calibrate a transferable polarizable force field parameter set for primary alcohols. J. Comput. Chem. 38 (8) (2017)
Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled M. Elbassioni, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau
Charge Group Partitioning in Biomolecular Simulation. J. Comput. Biol. 20 (3) (2013)
Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled M. Elbassioni, Alpeshkumar K. Malde, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau
Charge Group Partitioning in Biomolecular Simulation. RECOMB (2012)
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
New functionalities in the GROMOS biomolecular simulation software. J. Comput. Chem. 33 (3) (2012)
Stephanie B. A. De Beer, Harini Venkataraman, Daan P. Geerke, Chris Oostenbrink, Nico P. E. Vermeulen
Free Energy Calculations Give Insight into the Stereoselective Hydroxylation of α-Ionones by Engineered Cytochrome P450 BM3 Mutants. J. Chem. Inf. Model. 52 (8) (2012)
Daan P. Geerke, Sandra Luber, Koni H. Marti, Wilfred F. van Gunsteren
On the direct calculation of the free energy of quantization for molecular systems in the condensed phase. J. Comput. Chem. 30 (4) (2009)
Haibo Yu, Daan P. Geerke, Haiyan Liu, Wilfred F. van Gunsteren
Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models. J. Comput. Chem. 27 (13) (2006)
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
The GROMOS software for biomolecular simulation: GROMOS05. J. Comput. Chem. 26 (16) (2005)
G. Theodoor De Jong, Daan P. Geerke, Axel Diefenbach, Miquel Solà, F. Matthias Bickelhaupt
benchmark and DFT validation study. J. Comput. Chem. 26 (10) (2005)