Daan P. Geerke - researchr alias

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Viewing Publication 1 - 16 from 16

2023

2019

Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approachMartin S. Engler, Bertrand Caron, Lourens Veen, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau. almob, 14(1), 2019. [doi]

A Comparative Linear Interaction Energy and MM/PBSA Study on SIRT1-Ligand Binding Free Energy CalculationEko Aditya Rifai, Marc van Dijk, Nico P. E. Vermeulen, Arry Yanuar, Daan P. Geerke. jcisd, 59(9):4018-4033, 2019. [doi]

2018

Multiple-Choice Knapsack for Assigning Partial Atomic Charges in Drug-Like MoleculesMartin S. Engler, Bertrand Caron, Lourens Veen, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau. wabi 2018: [doi]

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 2Eko A. Rifai, Marc van Dijk, Nico P. E. Vermeulen, Daan P. Geerke. jcamd, 32(1):239-249, 2018. [doi]

2017

2013

Charge Group Partitioning in Biomolecular SimulationStefan Canzar, Mohammed El-Kebir, René Pool, Khaled M. Elbassioni, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau. jcb, 20(3):188-198, 2013. [doi]

2012

2009

On the direct calculation of the free energy of quantization for molecular systems in the condensed phaseDaan P. Geerke, Sandra Luber, Koni H. Marti, Wilfred F. van Gunsteren. jcc, 30(4):514-523, 2009. [doi]

2006

Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable modelsHaibo Yu 0003, Daan P. Geerke, Haiyan Liu, Wilfred F. van Gunsteren. jcc, 27(13):1494-1504, 2006. [doi]

2005

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