Siewert-Jan Marrink

Dr. Siewert-Jan Marrink

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Research Focus & Metrics

Academic Career Length

35Years (1992-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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15 June 2007 in The Journal of Physical Chemistry B
Verified
Journal Article
Closed access
SMSiewert-Jan Marrink
Siewert-Jan Marrink
HRH. Jelger Risselada
H. Jelger Risselada
SYSerge Yefimov
Serge Yefimov
DTD. Peter Tieleman
D. Peter Tieleman
AVAlex H. de Vries
Alex H. de Vries

16 April 2008 in Journal of Chemical Theory and Computation
Verified
Journal Article
Closed access
LMLuca Monticelli
Luca Monticelli
SKSenthil K. Kandasamy
Senthil K. Kandasamy
XPXavier Periole
Xavier Periole
Ronald LarsonRonald Larson
Ronald Larson
DTD. Peter Tieleman
D. Peter Tieleman
SMSiewert-Jan Marrink
Siewert-Jan Marrink

2 December 2003 in The Journal of Physical Chemistry B
Verified
Journal Article
Closed access
SMSiewert-Jan Marrink
Siewert-Jan Marrink
AVAlex H. de Vries
Alex H. de Vries
AMAlan E. Mark
Alan E. Mark

29 March 2021 in Nature Methods
Verified
Journal Article
Closed access
PDF file
PSPaulo Cesar Telles de Souza
Paulo Cesar Telles de Souza
RARiccardo Alessandri
Riccardo Alessandri
JBJonathan Barnoud
Jonathan Barnoud
STSebastian Thallmair
Sebastian Thallmair
IFIgnacio Faustino
Ignacio Faustino
SMSiewert-Jan Marrink
Siewert-Jan Marrink

28 November 2012 in Journal of Chemical Theory and Computation
Verified
Journal Article
Open access
DJDjurre H. de Jong
Djurre H. de Jong
GSGurpreet Singh
Gurpreet Singh
WBW.F. Drew Bennett
W.F. Drew Bennett
CAClement Arnarez
Clement Arnarez
TWTsjerk A. Wassenaar
Tsjerk A. Wassenaar
SMSiewert-Jan Marrink
Siewert-Jan Marrink
The Martini coarse-grained force field has been successfully used for simulating a wide range of (bio)molecular systems. Recent progress in our ability to test the model against fully atomistic force fields, however, has revealed some shortcomings. Most notable, phenylalanine and proline were too hydrophobic, and dimers formed by polar residues in apolar solvents did not bind strongly enough. Here, we reparametrize these residues either through reassignment of particle types or by introducing embedded charges. The new parameters are tested with respect to partitioning across a lipid bilayer, membrane binding of Wimley–White peptides, and dimerization free energy in solvents of different polarity. In addition, we improve some of the bonded terms in the Martini protein force field that lead to a more realistic length of α-helices and to improved numerical stability for polyalanine and glycine repeats. The new parameter set is denoted Martini version 2.2.

24 April 2015 in Journal of Chemical Theory and Computation
Verified
Journal Article
Closed access
TWTsjerk Wassenaar
Tsjerk Wassenaar
HIHelgi I. Ingólfsson
Helgi I. Ingólfsson
RBRainer A Böckmann
Rainer A Böckmann
DTD. Peter Tieleman
D. Peter Tieleman
SMSiewert-Jan Marrink
Siewert-Jan Marrink