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1

The MARTINI Coarse-Grained Force Field: Extension to Proteins

Monticelli, Luca, Kandasamy, Senthil K., Periole, Xavier, Larson, Ronald G., Tieleman, D. Peter, Marrink, Siewert-Jan

Journal:

Journal of Chemical Theory and Computation

Year:

2008

Language:

english

File:

PDF, 3.95 MB

english, 2008

2

Molecular dynamics simulation of a phospholipid membrane

Egbert Egberts, Siewert-Jan Marrink, Herman J. C. Berendsen

Journal:

European Biophysics Journal

Year:

1994

Language:

english

File:

PDF, 1.51 MB

english, 1994

3

The structural basis for peptide selection by the transport receptor OppA

Berntsson, Ronnie P-A, Doeven, Mark K, Fusetti, Fabrizia, Duurkens, Ria H, Sengupta, Durba, Marrink, Siewert-Jan, Thunnissen, Andy-Mark W H, Poolman, Bert, Slotboom, Dirk-Jan

Journal:

The EMBO Journal

Year:

2009

Language:

english

File:

PDF, 1.41 MB

english, 2009

4

A molecular dynamics study of the decane/water interface

van Buuren, Aldert R., Marrink, Siewert Jan, Berendsen, Herman J. C.

Journal:

Journal of Physical Chemistry

Year:

1993

Language:

english

File:

PDF, 845 KB

english, 1993

5

Toroidal pores formed by antimicrobial peptides show significant disorder

Durba Sengupta, Hari Leontiadou, Alan E. Mark, Siewert-Jan Marrink

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2008

Language:

english

File:

PDF, 4.57 MB

english, 2008

6

A Coarse-Grained Model for Polyethylene Oxide and Polyethylene Glycol: Conformation and Hydrodynamics

Lee, Hwankyu, de Vries, Alex H., Marrink, Siewert-Jan, Pastor, Richard W.

Journal:

Journal of Physical Chemistry B

Year:

2009

Language:

english

File:

PDF, 312 KB

english, 2009

7

Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition

Periole, Xavier, Cavalli, Marco, Marrink, Siewert-Jan, Ceruso, Marco A.

Journal:

Journal of Chemical Theory and Computation

Year:

2009

Language:

english

File:

PDF, 3.31 MB

english, 2009

8

A Structurally Flexible Protein Backbone for the MARTINI Coarse Grained Force Field

Periole, Xavier, Marrink, Siewert-Jan, Tieleman, Peter

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 51 KB

english, 2011

9

Simulations of the c -subunit of ATP-synthase reveal helix rearrangements

Sengupta, Durba, Rampioni, Aldo, Marrink, Siewert-Jan

Journal:

Molecular Membrame Biology

Year:

2009

Language:

english

File:

PDF, 5.36 MB

english, 2009

10

Characterisation of aqueous interfaces with different hydrophobicities by molecular dynamics

Aldert R. van Buuren, Siewert-Jan Marrink, Herman J.C. Berendsen

Journal:

Colloids and Surfaces A: Physicochemical and Engineering Aspects

Year:

1995

Language:

english

File:

PDF, 1.07 MB

english, 1995

11

Effects of bundling on the properties of the SPC water model

Marc Fuhrmans, Barbara P. Sanders, Siewert-Jan Marrink, Alex H. de Vries

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

2010

Language:

english

File:

PDF, 631 KB

english, 2010

12

A tool for the morphological analysis of mixtures of lipids and water in computer simulations

Marc Fuhrmans, Siewert-Jan Marrink

Journal:

Journal of Molecular Modeling

Year:

2011

Language:

english

File:

PDF, 875 KB

english, 2011

13

Methodological Issues in Lipid Bilayer Simulations

Anézo, Céline, de Vries, Alex H., Höltje, Hans-Dieter, Tieleman, D. Peter, Marrink, Siewert-Jan

Journal:

Journal of Physical Chemistry B

Year:

2003

Language:

english

File:

PDF, 179 KB

english, 2003

14

Simulation of water transport through a lipid membrane

Marrink, Siewert-Jan, Berendsen, Herman J. C.

Journal:

Journal of Physical Chemistry

Year:

1994

Language:

english

File:

PDF, 1.85 MB

english, 1994

15

Sphere-to-Rod Transitions of Nonionic Surfactant Micelles in Aqueous Solution Modeled by Molecular Dynamics Simulations

Velinova, Maria, Sengupta, Durba, Tadjer, Alia V., Marrink, Siewert-Jan

Journal:

Year:

2011

Language:

english

File:

PDF, 3.70 MB

english, 2011

16

Transmembrane helices can induce domain formation in crowded model membranes

Jan Domański, Siewert J. Marrink, Lars V. Schäfer

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2012

Language:

english

File:

PDF, 1.80 MB

english, 2012

17

Ion Transport across Transmembrane Pores

Leontiadou, Hari, Mark, Alan E., Marrink, Siewert-Jan

Journal:

Biophysical Journal

Year:

2007

Language:

english

File:

PDF, 431 KB

english, 2007

18

Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition

Marrink, Siewert-Jan, Peter Tieleman, D.

Journal:

Biophysical Journal

Year:

2002

Language:

english

File:

PDF, 937 KB

english, 2002

19

Simulation of MscL Gating in a Bilayer under Stress

Colombo, Giorgio, Marrink, Siewert Jan, Mark, Alan E.

Journal:

Biophysical Journal

Year:

2003

Language:

english

File:

PDF, 445 KB

english, 2003

20

Alternative Mechanisms for the Interaction of the Cell-Penetrating Peptides Penetratin and the TAT Peptide with Lipid Bilayers

Yesylevskyy, Semen, Marrink, Siewert-Jan, Mark, Alan E.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 2.12 MB

english, 2009

21

Areas of Monounsaturated Diacylphosphatidylcholines

Kučerka, Norbert, Gallová, Jana, Uhríková, Daniela, Balgavý, Pavol, Bulacu, Monica, Marrink, Siewert-Jan, Katsaras, John

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 666 KB

english, 2009

22

Lateral Pressure Profile and Curvature Frustration in Mechanosensitive Channel Gating

Ollila, Samuli O.H., Louhivuori, Martti, Marrink, Siewert-Jan, Vattulainen, Ilpo

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 83 KB

english, 2010

23

Towards Molecular Dynamics Simulations of Large Protein Complexes

de Jong, Djurre, Periole, Xavier, Marrink, Siewert Jan

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 128 KB

english, 2010

24

A Model of the Open Pore MscL Based on Experimental Data and Restrained Coarse Grained Simulations

Deplazes, Evelyne, Jayatilaka, Dylan, Louhivuori, Martti, Marrink, Siewert-Jan, Corry, Ben

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 55 KB

english, 2012

25

Adhesion Forces of Lipids in a Phospholipid Membrane Studied by Molecular Dynamics Simulations

Marrink, Siewert-Jan, Berger, Oliver, Tieleman, Peter, Jähnig, Fritz

Journal:

Biophysical Journal

Year:

1998

Language:

english

File:

PDF, 267 KB

english, 1998

26

Molecular View of Hexagonal Phase Formation in Phospholipid Membranes

Marrink, Siewert-Jan, Mark, Alan E.

Journal:

Biophysical Journal

Year:

2004

Language:

english

File:

PDF, 696 KB

english, 2004

27

Molecular Dynamics Simulations of Lipid Vesicle Fusion in Atomic Detail

Knecht, Volker, Marrink, Siewert-Jan

Journal:

Biophysical Journal

Year:

2007

Language:

english

File:

PDF, 2.11 MB

english, 2007

28

Structure of Spheroidal HDL Particles Revealed by Combined Atomistic and Coarse-Grained Simulations

Catte, Andrea, Patterson, James C., Bashtovyy, Denys, Jones, Martin K., Gu, Feifei, Li, Ling, Rampioni, Aldo, Sengupta, Durba, Vuorela, Timo, Niemelä, Perttu, Karttunen, Mikko, Marrink, Siewert Jan, V

Journal:

Biophysical Journal

Year:

2008

Language:

english

File:

PDF, 1.69 MB

english, 2008

29

Curvature-Dependent Elastic Properties of Liquid-Ordered Domains Result in Inverted Domain Sorting on Uniaxially Compressed Vesicles

Risselada, H. Jelger, Marrink, Siewert Jan, Müller, Marcus

Journal:

Physical Review Letters

Year:

2011

Language:

english

File:

PDF, 357 KB

english, 2011

30

Molecular dynamics simulation of a membrane/water interface: the ordering of water and its relation to the hydration force

Marrink, Siewert Jan, Berkowitz, Max, Berendsen, Herman J. C.

Journal:

Year:

1993

Language:

english

File:

PDF, 1.80 MB

english, 1993

31

Lipids Out of Equilibrium: Energetics of Desorption and Pore Mediated Flip-Flop

Tieleman, D. Peter, Marrink, Siewert-Jan

Journal:

Journal of the American Chemical Society

Year:

2006

Language:

english

File:

PDF, 1.80 MB

english, 2006

32

G Protein-Coupled Receptors Self-Assemble in Dynamics Simulations of Model Bilayers

Periole, Xavier, Huber, Thomas, Marrink, Siewert-Jan, Sakmar, Thomas P.

Journal:

Journal of the American Chemical Society

Year:

2007

Language:

english

File:

PDF, 553 KB

english, 2007

33

Simulation of Pore Formation in Lipid Bilayers by Mechanical Stress and Electric Fields

Tieleman, D. Peter, Leontiadou, Hari, Mark, Alan E., Marrink, Siewert-Jan

Journal:

Journal of the American Chemical Society

Year:

2003

Language:

english

File:

PDF, 954 KB

english, 2003

34

Low density lipoprotein: structure, dynamics, and interactions of apoB-100 with lipids

Murtola, Teemu, Vuorela, Timo A., Hyvönen, Marja T., Marrink, Siewert-Jan, Karttunen, Mikko, Vattulainen, Ilpo

Journal:

Year:

2011

Language:

english

File:

PDF, 415 KB

english, 2011

35

Cardiolipins at the Interface of Supercomplexes in the Respiratory Chain

Arnarez, Clement, Marrink, Siewert-Jan, Periole, Xavier

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 90 KB

english, 2014

36

MscL Gating In Liposomes

Louhivuori, Martti, Risselada, Jelger, van der Giessen, Erik, Marrink, Siewert-Jan

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 58 KB

english, 2009

37

“Multi-Hit” Action of Membrane Active Peptides: Towards Understanding Bacterial Cell Killing

Moiset, Gemma, Cirac, Anna D., Mika, Jacek T., Koçer, Armağan, Stuart, Marc C.A., Sengupta, Durba, Marrink, Siewert-Jan, Poolman, Bert

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 72 KB

english, 2012

38

Amyloid-Like Cross-Beta Structure Polymorphism: An Energetic Point of View

Periole, Xavier, Huber, Thomas, Sakmar, Thomas P., Marrink, Siewert-Jan

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 34 KB

english, 2010

39

Hybrid Simulations: Atomistic Peptides in Coarse Grained Solvent

Rzepiela, Andrzej J., Louhivuori, Martti, Marrink, Siewert Jan

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 51 KB

english, 2010

40

The Molecular Basis for Antimicrobial Activity of Pore-Forming Cyclic Peptides

Moiset, Gemma, Cirac, Anna D., Mika, Jacek T., Koçer, Armagan, Sengupta, Durba, Marrink, Siewert-Jan, Poolman, Bert

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 65 KB

english, 2011

41

Self-assembly and Equilibration of Bolalipid Membranes Studied by Molecular Dynamics Simulations

Bulacu, Monica, Marrink, Siewert Jan

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 32 KB

english, 2009

42

Development of Coarse-Grained Martini Model for Nucleic Acid Structures

Akhshi, Parisa, Uusitalo, Jaakko, Ingolfsson, Helgi, Marrink, Siewert-Jan, Tieleman, D. Peter

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 44 KB

english, 2014

43

Sensitivity of Coarse-Grained Mechano-Sensation

Louhivuori, Martti, Marrink, Siewert Jan

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 87 KB

english, 2011

44

Probing the Receptor Dimer Interfaces of G-Protein Coupled Receptor in Model Membranes

Periole, Xavier, Knepp, Adam M., Sakmar, Tom P., Marrink, Siewert-Jan, Huber, Thomas

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 86 KB

english, 2012

45

Covering All the Bases: A Martini Coarse-Grained Force Field for DNA

Uusitalo, Jaakko J., Ingólfsson, Helgi I., Marrink, Siewert-Jan

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 102 KB

english, 2013

46

Dynamic Assembly of the Receptor-G-Protein Signaling Complex

Huber, Thomas, Periole, Xavier, Knepp, Adam M., Marrink, Siewert-Jan, Mukhopadhyay, Parag, Sakmar, Thomas P.

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 57 KB

english, 2012

47

The Daft Approach for in Silico Prediction of Transmembrane Peptide Complexes

Wassenaar, Tsjerk A., Moussatova, Anastassiia, Marrink, Siewert-Jan, Tieleman, Peter

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 132 KB

english, 2013

48

Membrane Proteins-bilayer Interplay: Insights From Coarse-grained Self-assembly And Potential Of Mean Force Simulations Of Rhodopsin In Model Bilayers

Periole, Xavier, Huber, Thomas, Marrink, Siewert-Jan, Sakmar, Thomas P.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 34 KB

english, 2009

49

A Nano-Scavenger in Action: The Molecular Mechanism of Membrane Cholesterol Extraction by Cyclodextrins

Lopez, Cesar A., de Vries, Alex H., Jan Marrink, Siewert

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 95 KB

english, 2012

50

Mixing Martinis: Atomistic Simulations of MscL in a Coarse Grained Environment

Wassenaar, Tsjerk A., Schafer, Lars V., Ingolfsson, Helgi, Marrink, Siewert-Jan

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 107 KB

english, 2012

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