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2020 – today
- 2023
[j8]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
- [j7]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
- [j6]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
- [j5]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) - [j4]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
- [j3]Micha Werner, Jaap Schellekens, Peter Gijsbers, Marc van Dijk, Onno van den Akker, Karel Heynert:
The Delft-FEWS flow forecasting system. Environ. Model. Softw. 40: 65-77 (2013) - 2012
- [j2]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, Lucio Ferella, Antonio Rosato, Ivano Bertini, Torsten Herrmann, Hendrik R. A. Jonker, Anurag Bagaria, Victor Jaravine, Peter Güntert, Harald Schwalbe, Wim F. Vranken, Jurgen F. Doreleijers, Gert Vriend, Geerten W. Vuister, Daniel Franke, Alexey Kikhney, Dmitri I. Svergun, Rasmus H. Fogh, John M. C. Ionides, Ernest D. Laue, Chris A. E. M. Spronk, Simonas Jurksa, Marco Verlato, Simone Badoer, Stefano Dal Pra, Mirco Mazzucato, Eric Frizziero, Alexandre M. J. J. Bonvin:
WeNMR: Structural Biology on the Grid. J. Grid Comput. 10(4): 743-767 (2012) - 2011
- [c1]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, Lucio Ferella, Antonio Rosato, Ivano Bertini, Torsten Herrmann, Hendrik R. A. Jonker, Anurag Bagaria, Victor Jaravine, Peter Güntert, Harald Schwalbe, Wim F. Vranken, Jurgen F. Doreleijers, Gert Vriend, Geerten W. Vuister, Daniel Franke, Alexey Kikhney, Dmitri I. Svergun, Rasmus H. Fogh, John M. C. Ionides, Ernest D. Laue, Chris A. E. M. Spronk, Marco Verlato, Simone Badoer, Stefano Dal Pra, Mirco Mazzucato, Eric Frizziero, Alexandre M. J. J. Bonvin:
WeNMR: Structural Biology on the Grid. IWSG-Life 2011
2000 – 2009
- 2009
- [j1]Marc van Dijk, Alexandre M. J. J. Bonvin:
3D-DART: a DNA structure modelling server. Nucleic Acids Res. 37(Web-Server-Issue): 235-239 (2009)
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