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 (International Conference on Computational Science, 2003)

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)

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)

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)

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)

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)

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)

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)

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)

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)

Unbreaking Assemblies in Molecular Simulations with Periodic Boundaries. - Bart M. H. Bruininks; Tsjerk A. Wassenaar; Ilpo Vattulainen (J. Chem. Inf. Model., 2023)

The Relation Between the EVD or SVD of Summands and the EVD or SVD of the Sum. - Tsjerk A. Wassenaar (CoRR, 2024)