Backmapping triangulated surfaces to coarse-grained membrane models
Pezeshkian, Weria, König, Melanie, Wassenaar, Tsjerk A, Marrink, Siewert J
Published in Nature communications (08.05.2020)
Published in Nature communications (08.05.2020)
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Journal Article
Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models
Wassenaar, Tsjerk A, Pluhackova, Kristyna, Böckmann, Rainer A, Marrink, Siewert J, Tieleman, D. Peter
Published in Journal of chemical theory and computation (11.02.2014)
Published in Journal of chemical theory and computation (11.02.2014)
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Journal Article
Improved Parameters for the Martini Coarse-Grained Protein Force Field
de Jong, Djurre H, Singh, Gurpreet, Bennett, W. F. Drew, Arnarez, Clement, Wassenaar, Tsjerk A, Schäfer, Lars V, Periole, Xavier, Tieleman, D. Peter, Marrink, Siewert J
Published in Journal of chemical theory and computation (08.01.2013)
Published in Journal of chemical theory and computation (08.01.2013)
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Journal Article
LION/web: a web-based ontology enrichment tool for lipidomic data analysis
Molenaar, Martijn R, Jeucken, Aike, Wassenaar, Tsjerk A, van de Lest, Chris H A, Brouwers, Jos F, Helms, J Bernd
Published in Gigascience (01.06.2019)
Published in Gigascience (01.06.2019)
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Journal Article
Lipid–Protein Interactions Are Unique Fingerprints for Membrane Proteins
Corradi, Valentina, Mendez-Villuendas, Eduardo, Ingólfsson, Helgi I, Gu, Ruo-Xu, Siuda, Iwona, Melo, Manuel N, Moussatova, Anastassiia, DeGagné, Lucien J, Sejdiu, Besian I, Singh, Gurpreet, Wassenaar, Tsjerk A, Delgado Magnero, Karelia, Marrink, Siewert J, Tieleman, D. Peter
Published in ACS central science (27.06.2018)
Published in ACS central science (27.06.2018)
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Journal Article
Activation of the bacterial thermosensor DesK involves a serine zipper dimerization motif that is modulated by bilayer thickness
Cybulski, Larisa Estefanía, Ballering, Joost, Moussatova, Anastassiia, Inda, Maria Eugenia, Vazquez, Daniela B., Wassenaar, Tsjerk A., de Mendoza, Diego, Tieleman, D. Peter, Killian, J. Antoinette
Published in Proceedings of the National Academy of Sciences - PNAS (19.05.2015)
Published in Proceedings of the National Academy of Sciences - PNAS (19.05.2015)
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Journal Article
Synaptobrevin Transmembrane Domain Dimerization Studied by Multiscale Molecular Dynamics Simulations
Han, Jing, Pluhackova, Kristyna, Wassenaar, Tsjerk A., Böckmann, Rainer A.
Published in Biophysical journal (18.08.2015)
Published in Biophysical journal (18.08.2015)
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Journal Article
Structural Aspects of the ROS1 Kinase Domain and Oncogenic Mutations
Vilachã, Juliana F, Wassenaar, Tsjerk A, Marrink, Siewert J
Published in Crystals (Basel) (01.01.2024)
Published in Crystals (Basel) (01.01.2024)
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Journal Article
Martini 3: a general purpose force field for coarse-grained molecular dynamics
Souza, Paulo C T, Alessandri, Riccardo, Barnoud, Jonathan, Thallmair, Sebastian, Faustino, Ignacio, Grünewald, Fabian, Patmanidis, Ilias, Abdizadeh, Haleh, Bruininks, Bart M H, Wassenaar, Tsjerk A, Kroon, Peter C, Melcr, Josef, Nieto, Vincent, Corradi, Valentina, Khan, Hanif M, Domański, Jan, Javanainen, Matti, Martinez-Seara, Hector, Reuter, Nathalie, Best, Robert B, Vattulainen, Ilpo, Monticelli, Luca, Periole, Xavier, Tieleman, D Peter, de Vries, Alex H, Marrink, Siewert J
Published in Nature methods (01.04.2021)
Published in Nature methods (01.04.2021)
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Journal Article
Lipid Organization of the Plasma Membrane
Ingólfsson, Helgi I, Melo, Manuel N, van Eerden, Floris J, Arnarez, Clément, Lopez, Cesar A, Wassenaar, Tsjerk A, Periole, Xavier, de Vries, Alex H, Tieleman, D. Peter, Marrink, Siewert J
Published in Journal of the American Chemical Society (15.10.2014)
Published in Journal of the American Chemical Society (15.10.2014)
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Journal Article
Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations
Wassenaar, Tsjerk A, Ingólfsson, Helgi I, Böckmann, Rainer A, Tieleman, D. Peter, Marrink, Siewert J
Published in Journal of chemical theory and computation (12.05.2015)
Published in Journal of chemical theory and computation (12.05.2015)
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Journal Article
eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations
Capoferri, Luigi, van Dijk, Marc, Rustenburg, Ariën S., Wassenaar, Tsjerk A., Kooi, Derk P., Rifai, Eko A., Vermeulen, Nico P. E., Geerke, Daan P.
Published in Journal of cheminformatics (21.11.2017)
Published in Journal of cheminformatics (21.11.2017)
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Journal Article
Unbreaking Assemblies in Molecular Simulations with Periodic Boundaries
Bruininks, Bart M. H., Wassenaar, Tsjerk A., Vattulainen, Ilpo
Published in Journal of chemical information and modeling (12.06.2023)
Published in Journal of chemical information and modeling (12.06.2023)
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Journal Article
Nucleobase-functionalized graphene nanoribbons for accurate high-speed DNA sequencing
Paulechka, Eugene, Wassenaar, Tsjerk A, Kroenlein, Kenneth, Kazakov, Andrei, Smolyanitsky, Alex
Published in Nanoscale (01.01.2016)
Published in Nanoscale (01.01.2016)
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Journal Article
Statistical efficiency of methods for computing free energy of hydration
Yildirim, Ahmet, Wassenaar, Tsjerk A, van der Spoel, David
Published in The Journal of chemical physics (14.10.2018)
Published in The Journal of chemical physics (14.10.2018)
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