Siewert J. Marrink

Publication Activity (10 Years)

Years Active: 2010-2023
Publications (10 Years): 9

Top Topics

Protein Folding

Computationally Intensive

Top Venues

J. Chem. Inf. Model.

PLoS Comput. Biol.

J. Comput. Chem.

Publications

Cécile Hilpert, Louis Beranger, Paulo Cesar Telles de Souza, Petteri A. Vainikka, Vincent Nieto, Siewert J. Marrink, Luca Monticelli, Guillaume Launay
Facilitating CG Simulations with MAD: The MArtini Database Server. J. Chem. Inf. Model. 63 (3) (2023)
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. 63 (12) (2023)
Mariia Nemchinova, Josef Melcr, Tsjerk A. Wassenaar, Siewert J. Marrink, Albert Guskov
Asymmetric CorA Gating Mechanism as Observed by Molecular Dynamics Simulations. J. Chem. Inf. Model. 61 (5) (2021)
Carlos Ramírez-Palacios, Hein J. Wijma, Sebastian Thallmair, Siewert J. Marrink, Dick B. Janssen
Computational Prediction of ω-Transaminase Specificity by a Combination of Docking and Molecular Dynamics Simulations. J. Chem. Inf. Model. 61 (11) (2021)
Lisbeth Ravnkilde Kjølbye, Leonardo De Maria, Tsjerk A. Wassenaar, Haleh Abdizadeh, Siewert J. Marrink, Jesper Ferkinghoff-Borg, Birgit Schiøtt
General Protocol for Constructing Molecular Models of Nanodiscs. J. Chem. Inf. Model. 61 (6) (2021)
Fude Sun, Carsten F. E. Schroer, Carlos Ramírez-Palacios, Lida Xu, Shi-Zhong Luo, Siewert J. Marrink
Molecular mechanism for bidirectional regulation of CD44 for lipid raft affiliation by palmitoylations and PIP2. PLoS Comput. Biol. 16 (4) (2020)
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
CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides. J. Comput. Chem. 38 (27) (2017)
Ignacio Faustino, Siewert J. Marrink
cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations. Bioinform. 33 (23) (2017)
Djurre H. De Jong, Svetlana Baoukina, Helgi I. Ingólfsson, Siewert J. Marrink
Martini straight: Boosting performance using a shorter cutoff and GPUs. Comput. Phys. Commun. 199 (2016)
Jonathan Barnoud, Giulia Rossi, Siewert J. Marrink, Luca Monticelli
Hydrophobic Compounds Reshape Membrane Domains. PLoS Comput. Biol. 10 (10) (2014)
Hein J. Wijma, Siewert J. Marrink, Dick B. Janssen
Computationally Efficient and Accurate Enantioselectivity Modeling by Clusters of Molecular Dynamics Simulations. J. Chem. Inf. Model. 54 (7) (2014)
Nicolae Goga, Siewert J. Marrink, Ruxandra Cioromela, Florica Moldoveanu
GPU-SD and DPD parallelization for Gromacs tools for molecular dynamics simulations. BIBE (2012)
Evelyne Deplazes, Martti Louhivuori, Dylan Jayatilaka, Siewert J. Marrink, Ben Corry
Structural Investigation of MscL Gating Using Experimental Data and Coarse Grained MD Simulations. PLoS Comput. Biol. 8 (9) (2012)
Cesar A. López, Alex H. de Vries, Siewert J. Marrink
Molecular Mechanism of Cyclodextrin Mediated Cholesterol Extraction. PLoS Comput. Biol. 7 (3) (2011)
Djurre H. De Jong, Lars V. Schäfer, Alex H. de Vries, Siewert J. Marrink, Herman J. C. Berendsen, Helmut Grubmüller
Determining equilibrium constants for dimerization reactions from molecular dynamics simulations. J. Comput. Chem. 32 (9) (2011)
Semen O. Yesylevskyy, Lars V. Schäfer, Durba Sengupta, Siewert J. Marrink
Polarizable Water Model for the Coarse-Grained MARTINI Force Field. PLoS Comput. Biol. 6 (6) (2010)
Timo Vuorela, Andrea Catte, Perttu S. Niemelä, Anette Hall, Marja T. Hyvönen, Siewert J. Marrink, Mikko Karttunen, Ilpo Vattulainen
Role of Lipids in Spheroidal High Density Lipoproteins. PLoS Comput. Biol. 6 (10) (2010)
Andrzej J. Rzepiela, Lars V. Schäfer, Nicolae Goga, H. Jelger Risselada, Alex H. de Vries, Siewert J. Marrink
Reconstruction of atomistic details from coarse-grained structures. J. Comput. Chem. 31 (6) (2010)