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)

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)

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)

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)

Molecular Mechanism of Cyclodextrin Mediated Cholesterol Extraction. - Cesar A. López; Alex H. de Vries; Siewert J. Marrink (PLoS Comput. Biol., 2011)

GPU-SD and DPD parallelization for Gromacs tools for molecular dynamics simulations. - Nicolae Goga; Siewert J. Marrink; Ruxandra Cioromela; Florica Moldoveanu (BIBE, 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)

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)

Hydrophobic Compounds Reshape Membrane Domains. - Jonathan Barnoud; Giulia Rossi; Siewert J. Marrink; Luca Monticelli (PLoS Comput. Biol., 2014)

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)

cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations. - Ignacio Faustino; Siewert J. Marrink (Bioinform., 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 C. T. Souza; Jumin Lee; Dhilon S. Patel; Siewert J. Marrink; Yifei Qi; Syma Khalid; Wonpil Im (J. Comput. Chem., 2017)

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)

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)

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)

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)

Facilitating CG Simulations with MAD: The MArtini Database Server. - Cécile Hilpert; Louis Beranger; Paulo C. T. Souza; Petteri A. Vainikka; Vincent Nieto; Siewert J. Marrink; Luca Monticelli; Guillaume Launay (J. Chem. Inf. Model., 2023)

Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG. - Charly Empereur-mot; Kasper B. Pedersen; Riccardo Capelli; Martina Crippa; Cristina Caruso; Mattia Perrone; Paulo C. T. Souza; Siewert J. Marrink; Giovanni M. Pavan (J. Chem. Inf. Model., 2023)

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)

MartiniGlass: a Tool for Enabling Visualization of Coarse-Grained Martini Topologies. - Christopher Brasnett; Siewert J. Marrink (J. Chem. Inf. Model., 2025)