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2020 – today
- 2023
[j14]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): 357-371 (2023)
2010 – 2019
- 2019
- [j13]Martin S. Engler, Bertrand Caron, Lourens E. 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): 1:1-1:10 (2019) - [j12]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): 4018-4033 (2019) - 2018
- [j11]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): 239-249 (2018) - [c2]Martin S. Engler, Bertrand Caron, Lourens E. Veen, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau:
Multiple-Choice Knapsack for Assigning Partial Atomic Charges in Drug-Like Molecules. WABI 2018: 16:1-16:13 - 2017
- [j10]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): 508-517 (2017) - [j9]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): 58:1-58:13 (2017) - [j8]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): 2294-2308 (2017) - 2013
- [j7]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): 188-198 (2013) - 2012
- [j6]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): 340-353 (2012) - [j5]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): 2139-2148 (2012) - [c1]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: 29-43
2000 – 2009
- 2009
- [j4]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): 514-523 (2009) - 2006
- [j3]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): 1494-1504 (2006) - 2005
- [j2]G. Theodoor De Jong, Daan P. Geerke, Axel Diefenbach, Miquel Solà, Friedrich Matthias Bickelhaupt:
Oxidative addition of the ethane C-C bond to Pd. An ab initio benchmark and DFT validation study. J. Comput. Chem. 26(10): 1006-1020 (2005) - [j1]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): 1719-1751 (2005)
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