Tsjerk A. Wassenaar

According to our database, Tsjerk A. Wassenaar authored at least 12 papers between 2003 and 2023.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2023

Unbreaking Assemblies in Molecular Simulations with Periodic Boundaries.

Bart M. H. Bruininks, Tsjerk A. Wassenaar, Ilpo Vattulainen

J. Chem. Inf. Model., June, 2023

2022

Martinize2 and Vermouth: Unified Framework for Topology Generation.

Peter C. Kroon, Fabian Grünewald, Jonathan Barnoud, Marco van Tilburg, Paulo C. T. Souza, Tsjerk A. Wassenaar, Siewert-Jan Marrink

CoRR, 2022

2021

Asymmetric CorA Gating Mechanism as Observed by Molecular Dynamics Simulations.

Mariia Nemchinova, Josef Melcr, Tsjerk A. Wassenaar, Siewert J. Marrink, Albert Guskov

J. Chem. Inf. Model., 2021

General Protocol for Constructing Molecular Models of Nanodiscs.

Lisbeth Ravnkilde Kjølbye, Leonardo De Maria, Tsjerk A. Wassenaar, Haleh Abdizadeh, Siewert J. Marrink, Jesper Ferkinghoff-Borg, Birgit Schiøtt

J. Chem. Inf. Model., 2021

2018

Dopamine transporter oligomerization involves the scaffold domain, but spares the bundle domain.

Kumaresan Jayaraman, Alex N. Morley, Dániel Szöllosi, Tsjerk A. Wassenaar, Harald H. Sitte, Thomas Stockner

PLoS Comput. Biol., 2018

2017

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

2016

Dynamic Cholesterol-Conditioned Dimerization of the G Protein Coupled Chemokine Receptor Type 4.

Kristyna Pluhackova, Stefan Gahbauer, Franziska Kranz, Tsjerk A. Wassenaar, Rainer A. Böckmann

PLoS Comput. Biol., 2016

2012

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, 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

J. Grid Comput., 2012

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, 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

Proceedings of the 3rd International Workshop on Science Gateways for Life Sciences, 2011

2006

The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions.

Tsjerk A. Wassenaar, Alan E. Mark

J. Comput. Chem., 2006

2004

A method to obtain a near-minimal-volume molecular simulation of a macromolecule, using periodic boundary conditions and rotational constraints.

Henk Bekker, Jur P. van den Berg, Tsjerk A. Wassenaar

J. Comput. Chem., 2004

2003

Constructing a Near-Minimal-Volume Computational Box for Molecular Dynamics Simulations with Periodic Boundary Conditions.

Henk Bekker, Jur P. van den Berg, Tsjerk A. Wassenaar

Proceedings of the Computational Science - ICCS 2003, 2003