Tsjerk A. Wassenaar

14 papers Misc 1Journal 12Unranked 1
YearRankTypeTitle / Venue / Authors
2026 J jnl
Peptide-nanoparticle platforms for antisense therapeutics: A coarse-grained modeling approach to brain delivery.
Comput. Biol. Medicine
Burcu Yesildag Uner, Alper Demir, Pingkun Zhou, Ekim Z. Taskiran, Tsjerk A. Wassenaar
2024 J jnl
The Relation Between the EVD or SVD of Summands and the EVD or SVD of the Sum.
CoRR
Tsjerk A. Wassenaar
2023 J jnl
Unbreaking Assemblies in Molecular Simulations with Periodic Boundaries.
J. Chem. Inf. Model.
Bart M. H. Bruininks, Tsjerk A. Wassenaar, Ilpo Vattulainen
2022 J jnl
Martinize2 and Vermouth: Unified Framework for Topology Generation.
CoRR
Peter C. Kroon, Fabian Grünewald, Jonathan Barnoud, Marco van Tilburg, Paulo C. T. Souza, Tsjerk A. Wassenaar, Siewert-Jan Marrink
2021 J jnl
Asymmetric CorA Gating Mechanism as Observed by Molecular Dynamics Simulations.
J. Chem. Inf. Model.
Mariia Nemchinova, Josef Melcr, Tsjerk A. Wassenaar, Siewert J. Marrink, Albert Guskov
2021 J jnl
General Protocol for Constructing Molecular Models of Nanodiscs.
J. Chem. Inf. Model.
Lisbeth Ravnkilde Kjølbye, Leonardo De Maria, Tsjerk A. Wassenaar, Haleh Abdizadeh, Siewert J. Marrink, Jesper Ferkinghoff-Borg, Birgit Schiøtt
2018 J jnl
Dopamine transporter oligomerization involves the scaffold domain, but spares the bundle domain.
PLoS Comput. Biol.
Kumaresan Jayaraman, Alex N. Morley, Dániel Szöllosi, Tsjerk A. Wassenaar, Harald H. Sitte, Thomas Stockner
2017 J jnl
eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations.
J. Cheminformatics
Luigi Capoferri, Marc van Dijk, Ariën S. Rustenburg, Tsjerk A. Wassenaar, Derk P. Kooi, Eko Aditya Rifai, Nico P. E. Vermeulen, Daan P. Geerke
2016 J jnl
Dynamic Cholesterol-Conditioned Dimerization of the G Protein Coupled Chemokine Receptor Type 4.
PLoS Comput. Biol.
Kristyna Pluhackova, Stefan Gahbauer, Franziska Kranz, Tsjerk A. Wassenaar, Rainer A. Böckmann
2012 J jnl
WeNMR: Structural Biology on the Grid.
J. Grid Comput.
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
2011 — conf
WeNMR: Structural Biology on the Grid.
IWSG-Life
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
2006 J jnl
The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions.
J. Comput. Chem.
Tsjerk A. Wassenaar, Alan E. Mark
2004 J jnl
A method to obtain a near-minimal-volume molecular simulation of a macromolecule, using periodic boundary conditions and rotational constraints.
J. Comput. Chem.
Henk Bekker, Jur P. van den Berg, Tsjerk A. Wassenaar
2003 Misc conf
Constructing a Near-Minimal-Volume Computational Box for Molecular Dynamics Simulations with Periodic Boundary Conditions.
International Conference on Computational Science
Henk Bekker, Jur P. van den Berg, Tsjerk A. Wassenaar