A preliminary 3D model for cytochrome P450 2D6 constructed by homology model building. - Lucien M. H. Koymans; Nico P. E. Vermeulen; Allard Baarslag; Gabriëlle M. Donné-Op den Kelder (J. Comput. Aided Mol. Des., 1993)

Ab initio calculations on iron-porphyrin model systems for intermediates in the oxidative cycle of cytochrome P450s. - Marcel J. de Groot; Remco W. A. Havenith; H. Maarten Vinkers; Renate Zwaans; Nico P. E. Vermeulen; Joop H. van Lenthe (J. Comput. Aided Mol. Des., 1998)

Are Automated Molecular Dynamics Simulations and Binding Free Energy Calculations Realistic Tools in Lead Optimization? An Evaluation of the Linear Interaction Energy (LIE) Method. - Eva Stjernschantz; John Marelius; Carmen Medina; Micael Jacobsson; Nico P. E. Vermeulen; Chris Oostenbrink (J. Chem. Inf. Model., 2006)

Virtual Screening and Prediction of Site of Metabolism for Cytochrome P450 1A2 Ligands. - Poongavanam Vasanthanathan; Jozef Hritz; Olivier Taboureau; Lars Olsen; Flemming Steen Jørgensen; Nico P. E. Vermeulen; Chris Oostenbrink (J. Chem. Inf. Model., 2009)

Molecular dynamics simulations and free energy calculations on the enzyme 4-hydroxyphenylpyruvate dioxygenase. - Stephanie B. A. De Beer; Alice Glättli; Johannes Hutzler; Nico P. E. Vermeulen; Chris Oostenbrink (J. Comput. Chem., 2011)

Free Energy Calculations Give Insight into the Stereoselective Hydroxylation of α-Ionones by Engineered Cytochrome P450 BM3 Mutants. - Stephanie B. A. De Beer; Harini Venkataraman; Daan P. Geerke; Chris Oostenbrink; Nico P. E. Vermeulen (J. Chem. Inf. Model., 2012)

eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations. - Luigi Capoferri; Marc van Dijk; Ariën S. Rustenburg; Tsjerk A. Wassenaar; Derk P. Kooi; Eko Aditya Rifai; Nico P. E. Vermeulen; Daan P. Geerke (J. Cheminformatics, 2017)

Comprehensive and Automated Linear Interaction Energy Based Binding-Affinity Prediction for Multifarious Cytochrome P450 Aromatase Inhibitors. - Marc van Dijk; Antonius ter Laak; Jörg D. Wichard; Luigi Capoferri; Nico P. E. Vermeulen; Daan P. Geerke (J. Chem. Inf. Model., 2017)

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. - Eko Aditya Rifai; Marc van Dijk; Nico P. E. Vermeulen; Daan P. Geerke (J. Comput. Aided Mol. Des., 2018)

A Comparative Linear Interaction Energy and MM/PBSA Study on SIRT1-Ligand Binding Free Energy Calculation. - Eko Aditya Rifai; Marc van Dijk; Nico P. E. Vermeulen; Arry Yanuar; Daan P. Geerke (J. Chem. Inf. Model., 2019)