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Journal Articles
- 2019
[j10]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
- [j9]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) - 2017
- [j8]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) - [j7]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) - 2012
- [j6]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) - 2011
- [j5]Stephanie B. A. De Beer, Alice Glättli, Johannes Hutzler, Nico P. E. Vermeulen, Chris Oostenbrink:
Molecular dynamics simulations and free energy calculations on the enzyme 4-hydroxyphenylpyruvate dioxygenase. J. Comput. Chem. 32(10): 2160-2169 (2011) - 2009
- [j4]Poongavanam Vasanthanathan, Jozef Hritz, Olivier Taboureau, Lars Olsen, Flemming Steen Jørgensen, Nico P. E. Vermeulen, Chris Oostenbrink:
Virtual Screening and Prediction of Site of Metabolism for Cytochrome P450 1A2 Ligands. J. Chem. Inf. Model. 49(1): 43-52 (2009) - 2006
- [j3]Eva Stjernschantz, John Marelius, Carmen Medina, Micael Jacobsson, Nico P. E. Vermeulen, Chris Oostenbrink:
Are Automated Molecular Dynamics Simulations and Binding Free Energy Calculations Realistic Tools in Lead Optimization? An Evaluation of the Linear Interaction Energy (LIE) Method. J. Chem. Inf. Model. 46(5): 1972-1983 (2006) - 1998
- [j2]Marcel J. de Groot, Remco W. A. Havenith, H. Maarten Vinkers, Renate Zwaans, Nico P. E. Vermeulen, Joop H. van Lenthe:
Ab initio calculations on iron-porphyrin model systems for intermediates in the oxidative cycle of cytochrome P450s. J. Comput. Aided Mol. Des. 12(2): 183-193 (1998) - 1993
- [j1]Lucien M. H. Koymans, Nico P. E. Vermeulen, Allard Baarslag, Gabriëlle M. Donné-Op den Kelder:
A preliminary 3D model for cytochrome P450 2D6 constructed by homology model building. J. Comput. Aided Mol. Des. 7(3): 281-289 (1993)
Coauthor Index
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