Siewert J. Marrink

20 papers C 1Journal 19
YearRankTypeTitle / Venue / Authors
2025 J jnl
MartiniGlass: a Tool for Enabling Visualization of Coarse-Grained Martini Topologies.
J. Chem. Inf. Model.
Christopher Brasnett, Siewert J. Marrink
2025 J jnl
Systematic Approach to Parametrization of Disaccharides for the Martini 3 Coarse-Grained Force Field.
J. Chem. Inf. Model.
Astrid F. Brandner, Iain Peter Shand Smith, Siewert J. Marrink, Paulo C. T. Souza, Syma Khalid
2023 J jnl
Automatic Optimization of Lipid Models in the Martini Force Field Using
J. Chem. Inf. Model.
Charly Empereur-mot, Kasper B. Pedersen, Riccardo Capelli, Martina Crippa, Cristina Caruso, Mattia Perrone, Paulo C. T. Souza, Siewert J. Marrink, Giovanni M. Pavan
2023 J jnl
Facilitating CG Simulations with MAD: The MArtini Database Server.
J. Chem. Inf. Model.
Cécile Hilpert, Louis Beranger, Paulo C. T. Souza, Petteri A. Vainikka, Vincent Nieto, Siewert J. Marrink, Luca Monticelli, Guillaume Launay
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
Computational Prediction of ω-Transaminase Specificity by a Combination of Docking and Molecular Dynamics Simulations.
J. Chem. Inf. Model.
Carlos Ramírez-Palacios, Hein J. Wijma, Sebastian Thallmair, Siewert J. Marrink, Dick B. Janssen
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
2020 J jnl
Molecular mechanism for bidirectional regulation of CD44 for lipid raft affiliation by palmitoylations and PIP2.
PLoS Comput. Biol.
Fude Sun, Carsten F. E. Schroer, Carlos Ramírez-Palacios, Lida Xu, Shi-Zhong Luo, Siewert J. Marrink
2017 J jnl
CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides.
J. Comput. Chem.
Pin-Chia Hsu, Bart M. H. Bruininks, Damien Jefferies, Paulo C. T. Souza, Jumin Lee, Dhilon S. Patel, Siewert J. Marrink, Yifei Qi, Syma Khalid, Wonpil Im
2017 J jnl
cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations.
Bioinform.
Ignacio Faustino, Siewert J. Marrink
2016 J jnl
Martini straight: Boosting performance using a shorter cutoff and GPUs.
Comput. Phys. Commun.
Djurre H. De Jong, Svetlana Baoukina, Helgi I. Ingólfsson, Siewert J. Marrink
2014 J jnl
Computationally Efficient and Accurate Enantioselectivity Modeling by Clusters of Molecular Dynamics Simulations.
J. Chem. Inf. Model.
Hein J. Wijma, Siewert J. Marrink, Dick B. Janssen
2014 J jnl
Hydrophobic Compounds Reshape Membrane Domains.
PLoS Comput. Biol.
Jonathan Barnoud, Giulia Rossi, Siewert J. Marrink, Luca Monticelli
2012 C conf
GPU-SD and DPD parallelization for Gromacs tools for molecular dynamics simulations.
BIBE
Nicolae Goga, Siewert J. Marrink, Ruxandra Cioromela, Florica Moldoveanu
2012 J jnl
Structural Investigation of MscL Gating Using Experimental Data and Coarse Grained MD Simulations.
PLoS Comput. Biol.
Evelyne Deplazes, Martti Louhivuori, Dylan Jayatilaka, Siewert J. Marrink, Ben Corry
2011 J jnl
Determining equilibrium constants for dimerization reactions from molecular dynamics simulations.
J. Comput. Chem.
Djurre H. De Jong, Lars V. Schäfer, Alex H. de Vries, Siewert J. Marrink, Herman J. C. Berendsen, Helmut Grubmüller
2011 J jnl
Molecular Mechanism of Cyclodextrin Mediated Cholesterol Extraction.
PLoS Comput. Biol.
Cesar A. López, Alex H. de Vries, Siewert J. Marrink
2010 J jnl
Polarizable Water Model for the Coarse-Grained MARTINI Force Field.
PLoS Comput. Biol.
Semen O. Yesylevskyy, Lars V. Schäfer, Durba Sengupta, Siewert J. Marrink
2010 J jnl
Reconstruction of atomistic details from coarse-grained structures.
J. Comput. Chem.
Andrzej J. Rzepiela, Lars V. Schäfer, Nicolae Goga, H. Jelger Risselada, Alex H. de Vries, Siewert J. Marrink
2010 J jnl
Role of Lipids in Spheroidal High Density Lipoproteins.
PLoS Comput. Biol.
Timo Vuorela, Andrea Catte, Perttu S. Niemelä, Anette Hall, Marja T. Hyvönen, Siewert J. Marrink, Mikko Karttunen, Ilpo Vattulainen