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Daan P. Geerke
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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)
Coauthor Index
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last updated on 2024-05-08 21:02 CEST by the dblp team
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