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Employment (2)

Hanze University of Applied Sciences: Groningen, NL

2013-11-01 to present (Bioinformatics)
Employment
Source: Self-asserted source
Tsjerk Wassenaar

University of Groningen: Groningen, Groningen, NL

2010-01-01 to present
Employment
Source: Self-asserted source
Tsjerk Wassenaar

Works (48)

An integrative modelling approach to the mitochondrial cristae

2024-09-23 | Preprint
DOI: 10.1101/2024.09.23.613389
Contributors: Chelsea M. Brown; Marieke S. S. Westendorp; Rubi Zarmiento-Garcia; Jan A. Stevens; Sarah L. Rouse; Siewert J. Marrink; Tsjerk A. Wassenaar
Source: check_circle
Crossref

Structural Aspects of the ROS1 Kinase Domain and Oncogenic Mutations

Crystals
2024-01-23 | Journal article
DOI: 10.3390/cryst14020106
Contributors: Juliana F. Vilachã; Tsjerk A. Wassenaar; Siewert J. Marrink
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Unbreaking Assemblies in Molecular Simulations with Periodic Boundaries

Journal of Chemical Information and Modeling
2023-06-12 | Journal article
DOI: 10.1021/acs.jcim.2c01574
Contributors: Bart M. H. Bruininks; Tsjerk A. Wassenaar; Ilpo Vattulainen
Source: check_circle
Crossref

Sequential Voxel-Based Leaflet Segmentation of Complex Lipid Morphologies

Journal of Chemical Theory and Computation
2021-12-14 | Journal article
DOI: 10.1021/acs.jctc.1c00446
Contributors: Bart M. H. Bruininks; Albert S. Thie; Paulo C. T. Souza; Tsjerk A. Wassenaar; Shirin Faraji; Siewert J. Marrink
Source: check_circle
Crossref

Retinyl esters form lipid droplets independently of triacylglycerol and seipin

Journal of Cell Biology
2021-10-04 | Journal article
DOI: 10.1083/jcb.202011071
Contributors: Martijn R. Molenaar; Kamlesh K. Yadav; Alexandre Toulmay; Tsjerk A. Wassenaar; Muriel C. Mari; Lucie Caillon; Aymeric Chorlay; Ivan E. Lukmantara; Maya W. Haaker; Richard W. Wubbolts et al.
Source: check_circle
Crossref

General Protocol for Constructing Molecular Models of Nanodiscs

Journal of Chemical Information and Modeling
2021-06-28 | Journal article
DOI: 10.1021/acs.jcim.1c00157
Contributors: Lisbeth R. Kjølbye; Leonardo De Maria; Tsjerk A. Wassenaar; Haleh Abdizadeh; Siewert J. Marrink; Jesper Ferkinghoff-Borg; Birgit Schiøtt
Source: check_circle
Crossref

Backmapping triangulated surfaces to coarse-grained membrane models

Nature communications
2020 | Journal article
DOI: 10.1038/s41467-020-16094-y
Part of ISSN: 2041-1723
Source: Self-asserted source
Tsjerk Wassenaar

Charge-dependent interactions of monomeric and filamentous actin with lipid bilayers

Proceedings of the National Academy of Sciences of the United States of America
2020 | Journal article
DOI: 10.1073/pnas.1914884117
Part of ISSN: 0027-8424
Source: Self-asserted source
Tsjerk Wassenaar
grade
Preferred source (of 2)‎

Lipid-dependent conformational landscape of the ErbB2 growth factor receptor dimers

Chemistry and physics of lipids
2020 | Journal article
DOI: 10.1016/j.chemphyslip.2020.104911
Part of ISSN: 0009-3084
Source: Self-asserted source
Tsjerk Wassenaar

Structural characterization of supramolecular hollow nanotubes with atomistic simulations and SAXS

Physical chemistry chemical physics : PCCP
2020 | Journal article
DOI: 10.1039/d0cp03282d
Part of ISSN: 1463-9076
Source: Self-asserted source
Tsjerk Wassenaar

Structural Characterization of Supramolecular Hollow Nanotubes with Atomistic Simulations and SAXS
Source: Self-asserted source
Tsjerk Wassenaar

Lecithin:Retinol Acyl Transferase (LRAT) induces the formation of lipid droplets

2019 | Other
DOI: 10.1101/733931
Source: Self-asserted source
Tsjerk Wassenaar
grade
Preferred source (of 2)‎

LION/web: a web-based ontology enrichment tool for lipidomic data analysis

GigaScience
2019 | Journal article
DOI: 10.1093/gigascience/giz061
Part of ISSN: 2047-217X
Source: Self-asserted source
Tsjerk Wassenaar
grade
Preferred source (of 2)‎

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

PLoS computational biology
2018 | Journal article
DOI: 10.1371/journal.pcbi.1006229
Part of ISSN: 1553-734X
Source: Self-asserted source
Tsjerk Wassenaar

LION/web: a web-based ontology enrichment tool for lipidomic data analysis

2018 | Other
DOI: 10.1101/398040
Source: Self-asserted source
Tsjerk Wassenaar

Lipid-Protein Interactions Are Unique Fingerprints for Membrane Proteins

ACS central science
2018 | Journal article
DOI: 10.1021/acscentsci.8b00143
Part of ISSN: 2374-7943
Source: Self-asserted source
Tsjerk Wassenaar

Statistical efficiency of methods for computing free energy of hydration

The Journal of chemical physics
2018 | Journal article
DOI: 10.1063/1.5041835
Part of ISSN: 0021-9606
Source: Self-asserted source
Tsjerk Wassenaar
grade
Preferred source (of 2)‎

eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations

Journal of cheminformatics
2017 | Journal article
DOI: 10.1186/s13321-017-0243-x
Part of ISSN: 1758-2946
Source: Self-asserted source
Tsjerk Wassenaar
grade
Preferred source (of 2)‎

Lipid-protein interactions are unique fingerprints for membrane proteins

2017 | Other
DOI: 10.1101/191486
Source: Self-asserted source
Tsjerk Wassenaar

A MoS2-Based Capacitive Displacement Sensor for DNA Sequencing

ACS nano
2016 | Journal article
DOI: 10.1021/acsnano.6b05274
Part of ISSN: 1936-0851
Source: Self-asserted source
Tsjerk Wassenaar

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

PLoS computational biology
2016 | Journal article
DOI: 10.1371/journal.pcbi.1005169
Part of ISSN: 1553-734X
Source: Self-asserted source
Tsjerk Wassenaar
grade
Preferred source (of 2)‎

Nucleobase-functionalized graphene nanoribbons for accurate high-speed DNA sequencing

Nanoscale
2016 | Journal article
DOI: 10.1039/c5nr07061a
Part of ISSN: 2040-3364
Source: Self-asserted source
Tsjerk Wassenaar

Activation of the bacterial thermosensor DesK involves a serine zipper dimerization motif that is modulated by bilayer thickness

Proceedings of the National Academy of Sciences of the United States of America
2015 | Journal article
DOI: 10.1073/pnas.1422446112
Part of ISSN: 0027-8424
Source: Self-asserted source
Tsjerk Wassenaar

Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations

Biochimica et biophysica acta
2015 | Journal article
DOI: 10.1016/j.bbamem.2015.02.025
Part of ISSN: 0006-3002
Source: Self-asserted source
Tsjerk Wassenaar

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations

Journal of chemical theory and computation
2015 | Journal article
DOI: 10.1021/acs.jctc.5b00209
Part of ISSN: 1549-9618
Source: Self-asserted source
Tsjerk Wassenaar

High-Throughput Simulations of Dimer and Trimer Assembly of Membrane Proteins. The DAFT Approach

Journal of chemical theory and computation
2015 | Journal article
DOI: 10.1021/ct5010092
Part of ISSN: 1549-9618
Source: Self-asserted source
Tsjerk Wassenaar

Molecular dynamics study of the effect of active site protonation on Helicobacter pylori 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase

European biophysics journal : EBJ
2015 | Journal article
DOI: 10.1007/s00249-015-1067-0
Part of ISSN: 0175-7571
Source: Self-asserted source
Tsjerk Wassenaar

Probing binding sites and mechanisms of action of an I(Ks) activator by computations and experiments

Biophysical journal
2015 | Journal article
DOI: 10.1016/j.bpj.2014.10.059
Part of ISSN: 0006-3495
Source: Self-asserted source
Tsjerk Wassenaar

Spontaneous adsorption of coiled-coil model peptides K and E to a mixed lipid bilayer

The journal of physical chemistry. B
2015 | Journal article
DOI: 10.1021/acs.jpcb.5b00434
Part of ISSN: 1520-6106
Source: Self-asserted source
Tsjerk Wassenaar

Synaptobrevin Transmembrane Domain Dimerization Studied by Multiscale Molecular Dynamics Simulations

Biophysical journal
2015 | Journal article
DOI: 10.1016/j.bpj.2015.06.049
Part of ISSN: 0006-3495
Source: Self-asserted source
Tsjerk Wassenaar

Thermodynamic and kinetic characterization of transmembrane helix association

Physical chemistry chemical physics : PCCP
2015 | Journal article
DOI: 10.1039/c4cp03732d
Part of ISSN: 1463-9076
Source: Self-asserted source
Tsjerk Wassenaar

Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models

Journal of chemical theory and computation
2014 | Journal article
DOI: 10.1021/ct400617g
Part of ISSN: 1549-9618
Source: Self-asserted source
Tsjerk Wassenaar

Lipid organization of the plasma membrane

Journal of the American Chemical Society
2014 | Journal article
DOI: 10.1021/ja507832e
Part of ISSN: 0002-7863
Source: Self-asserted source
Tsjerk Wassenaar

Molecular dynamics investigation of Helicobacter pylori chemotactic protein CheY1 and two mutants

Journal of molecular modeling
2014 | Journal article
DOI: 10.1007/s00894-014-2212-x
Part of ISSN: 1610-2940
Source: Self-asserted source
Tsjerk Wassenaar

The effect of triple glutamic mutations E9Q/E194Q/E204Q on the structural stability of bacteriorhodopsin

The FEBS journal
2014 | Journal article
DOI: 10.1111/febs.12694
Part of ISSN: 1742-464X
Source: Self-asserted source
Tsjerk Wassenaar

X-ray structure, thermodynamics, elastic properties and MD simulations of cardiolipin/dimyristoylphosphatidylcholine mixed membranes

Chemistry and physics of lipids
2014 | Journal article
DOI: 10.1016/j.chemphyslip.2013.12.010
Part of ISSN: 0009-3084
Source: Self-asserted source
Tsjerk Wassenaar

Improved Parameters for the Martini Coarse-Grained Protein Force Field

Journal of chemical theory and computation
2013 | Journal article
DOI: 10.1021/ct300646g
Part of ISSN: 1549-9618
Source: Self-asserted source
Tsjerk Wassenaar

Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations

The journal of physical chemistry. B
2013 | Journal article
DOI: 10.1021/jp311533p
Part of ISSN: 1520-6106
Source: Self-asserted source
Tsjerk Wassenaar

Molecular dynamics simulations of membrane proteins

Methods in molecular biology (Clifton, N.J.)
2013 | Journal article
DOI: 10.1007/978-1-62703-487-6_6
Part of ISSN: 1064-3745
Source: Self-asserted source
Tsjerk Wassenaar

A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations

Journal of chemical theory and computation
2012 | Journal article
DOI: 10.1021/ct300102d
Part of ISSN: 1549-9618
Source: Self-asserted source
Tsjerk Wassenaar

SQUEEZE-E: The Optimal Solution for Molecular Simulations with Periodic Boundary Conditions

Journal of chemical theory and computation
2012 | Journal article
DOI: 10.1021/ct3000662
Part of ISSN: 1549-9618
Source: Self-asserted source
Tsjerk Wassenaar

The eNMR platform for structural biology

Journal of structural and functional genomics
2010 | Journal article
DOI: 10.1007/s10969-010-9084-9
Part of ISSN: 1345-711X
Source: Self-asserted source
Tsjerk Wassenaar

Calcium binding to the purple membrane: A molecular dynamics study

Proteins
2009 | Journal article
DOI: 10.1002/prot.22182
Part of ISSN: 0887-3585
Source: Self-asserted source
Tsjerk Wassenaar

The conformation of the extracellular binding domain of Death Receptor 5 in the presence and absence of the activating ligand TRAIL: a molecular dynamics study

Proteins
2008 | Journal article
DOI: 10.1002/prot.21541
Part of ISSN: 0887-3585
Source: Self-asserted source
Tsjerk Wassenaar

HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets

Proteins
2007 | Journal article
DOI: 10.1002/prot.21723
Part of ISSN: 0887-3585
Source: Self-asserted source
Tsjerk Wassenaar

How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?

The journal of physical chemistry. B
2007 | Journal article
DOI: 10.1021/jp068580v
Part of ISSN: 1520-6106
Source: Self-asserted source
Tsjerk Wassenaar

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

Journal of computational chemistry
2006 | Journal article
DOI: 10.1002/jcc.20341
Part of ISSN: 0192-8651
Source: Self-asserted source
Tsjerk Wassenaar

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

Journal of computational chemistry
2004 | Journal article
DOI: 10.1002/jcc.20050
Part of ISSN: 0192-8651
Source: Self-asserted source
Tsjerk Wassenaar

Peer review (15 reviews for 5 publications/grants)

Review activity for Biophysical journal. (1)
Review activity for Communications chemistry. (1)
Review activity for Journal of chemical information and modeling. (6)
Review activity for Journal of chemical theory and computation : (4)
Review activity for The journal of physical chemistry. (3)
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