3D-DART: a DNA structure modelling server. - Marc van Dijk; Alexandre M. J. J. Bonvin (Nucleic Acids Res., 2009)

WeNMR: Structural Biology on the Grid. - Tsjerk A. Wassenaar; Marc van Dijk; Nuno Loureiro-Ferreira; Gijs van der Schot; Sjoerd Jacob de Vries; Christophe Schmitz; Johan van der Zwan; Rolf Boelens; Andrea Giachetti 002; Lucio Ferella; Antonio Rosato; Ivano Bertini; et al. (IWSG-Life, 2011)

WeNMR: Structural Biology on the Grid. - Tsjerk A. Wassenaar; Marc van Dijk; Nuno Loureiro-Ferreira; Gijs van der Schot; Sjoerd Jacob de Vries; Christophe Schmitz; Johan van der Zwan; Rolf Boelens; Andrea Giachetti 002; Lucio Ferella; Antonio Rosato; Ivano Bertini; et al. (J. Grid Comput., 2012)

The Delft-FEWS flow forecasting system. - Micha Werner; Jaap Schellekens; Peter Gijsbers; Marc van Dijk; Onno van den Akker; Karel Heynert (Environ. Model. Softw., 2013)

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)

OFraMP: a fragment-based tool to facilitate the parametrization of large molecules. - 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; et al. (J. Comput. Aided Mol. Des., 2023)