Siewert J. Marrink

According to our database, Siewert J. Marrink authored at least 20 papers between 2010 and 2025.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2025

Systematic Approach to Parametrization of Disaccharides for the Martini 3 Coarse-Grained Force Field.

Astrid F. Brandner, Iain Peter Shand Smith, Siewert J. Marrink, Paulo C. T. Souza, Syma Khalid

J. Chem. Inf. Model., 2025

2023

Automatic Optimization of Lipid Models in the Martini Force Field Using <i>SwarmCG</i>.

Charly Empereur-mot, Kasper B. Pedersen, Riccardo Capelli, Martina Crippa, Cristina Caruso, Mattia Perrone, Paulo Cesar Telles de Souza, Siewert J. Marrink, Giovanni M. Pavan

J. Chem. Inf. Model., June, 2023

Facilitating CG Simulations with MAD: The MArtini Database Server.

Cécile Hilpert, Louis Beranger, Paulo Cesar Telles de Souza, Petteri A. Vainikka, Vincent Nieto, Siewert J. Marrink, Luca Monticelli, Guillaume Launay

J. Chem. Inf. Model., February, 2023

2022

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

2021

Computational Prediction of ω-Transaminase Specificity by a Combination of Docking and Molecular Dynamics Simulations.

Carlos Ramírez-Palacios, Hein J. Wijma, Sebastian Thallmair, Siewert J. Marrink, Dick B. Janssen

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

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

2020

Molecular mechanism for bidirectional regulation of CD44 for lipid raft affiliation by palmitoylations and PIP2.

Fude Sun, Carsten F. E. Schroer, Carlos Ramírez-Palacios, Lida Xu, Shi-Zhong Luo, Siewert J. Marrink

PLoS Comput. Biol., 2020

2017

CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides.

Pin-Chia Hsu, Bart M. H. Bruininks, Damien Jefferies, Paulo Cesar Telles de Souza, Jumin Lee, Dhilon S. Patel, Siewert J. Marrink, Yifei Qi, Syma Khalid, Wonpil Im

J. Comput. Chem., 2017

cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations.

Ignacio Faustino, Siewert J. Marrink

Bioinform., 2017

2016

Martini straight: Boosting performance using a shorter cutoff and GPUs.

Djurre H. De Jong, Svetlana Baoukina, Helgi I. Ingólfsson, Siewert J. Marrink

Comput. Phys. Commun., 2016

2014

Hydrophobic Compounds Reshape Membrane Domains.

Jonathan Barnoud, Giulia Rossi, Siewert J. Marrink, Luca Monticelli

PLoS Comput. Biol., 2014

Computationally Efficient and Accurate Enantioselectivity Modeling by Clusters of Molecular Dynamics Simulations.

Hein J. Wijma, Siewert J. Marrink, Dick B. Janssen

J. Chem. Inf. Model., 2014

2012

Structural Investigation of MscL Gating Using Experimental Data and Coarse Grained MD Simulations.

Evelyne Deplazes, Martti Louhivuori, Dylan Jayatilaka, Siewert J. Marrink, Ben Corry

PLoS Comput. Biol., 2012

GPU-SD and DPD parallelization for Gromacs tools for molecular dynamics simulations.

Nicolae Goga, Siewert J. Marrink, Ruxandra Cioromela, Florica Moldoveanu

Proceedings of the 12th IEEE International Conference on Bioinformatics & Bioengineering, 2012

2011

Molecular Mechanism of Cyclodextrin Mediated Cholesterol Extraction.

Cesar A. López, Alex H. de Vries, Siewert J. Marrink

PLoS Comput. Biol., 2011

Determining equilibrium constants for dimerization reactions from molecular dynamics simulations.

Djurre H. De Jong, Lars V. Schäfer, Alex H. de Vries, Siewert J. Marrink, Herman J. C. Berendsen, Helmut Grubmüller

J. Comput. Chem., 2011

2010

Polarizable Water Model for the Coarse-Grained MARTINI Force Field.

Semen O. Yesylevskyy, Lars V. Schäfer, Durba Sengupta, Siewert J. Marrink

PLoS Comput. Biol., 2010

Role of Lipids in Spheroidal High Density Lipoproteins.

Timo Vuorela, Andrea Catte, Perttu S. Niemelä, Anette Hall, Marja T. Hyvönen, Siewert J. Marrink, Mikko Karttunen, Ilpo Vattulainen

PLoS Comput. Biol., 2010

Reconstruction of atomistic details from coarse-grained structures.

Andrzej J. Rzepiela, Lars V. Schäfer, Nicolae Goga, H. Jelger Risselada, Alex H. de Vries, Siewert J. Marrink

J. Comput. Chem., 2010