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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

Improved Parameters for the Martini Coarse-Grained Protein Force Field

de Jong, Djurre H., Singh, Gurpreet, Bennett, W. F. Drew, Arnarez, Clement, Wassenaar, Tsjerk A., Schäfer, Lars V., Periole, Xavier, Tieleman, D. Peter, Marrink, Siewert J.

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 2.97 MB

english, 2013

3

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

4

In Silico Design of Robust Bolalipid Membranes

Bulacu, Monica, Périole, Xavier, Marrink, Siewert J.

Journal:

Biomacromolecules

Year:

2012

Language:

english

File:

PDF, 6.99 MB

english, 2012

5

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

6

Interplay of G Protein-Coupled Receptors with the Membrane: Insights from Supra-Atomic Coarse Grain Molecular Dynamics Simulations

Periole, Xavier

Journal:

Chemical Reviews

Year:

2016

Language:

english

File:

PDF, 17.83 MB

english, 2016

7

Probing the free energy landscape of the FBP28WW domain using multiple techniques

Xavier Periole, Lucy R. Allen, Kamil Tamiola, Alan E. Mark, Emanuele Paci

Journal:

Journal of Computational Chemistry

Year:

2009

Language:

english

File:

PDF, 807 KB

english, 2009

8

Molecular dynamics simulations from putative transition states of α-spectrin SH3 domain

Xavier Periole, Michele Vendruscolo, Alan E. Mark

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2007

Language:

english

File:

PDF, 945 KB

english, 2007

9

Refining homology models by combining replica-exchange molecular dynamics and statistical potentials

Jiang Zhu, Hao Fan, Xavier Periole, Barry Honig, Alan E. Mark

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 953 KB

english, 2008

10

Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: Application in the refinement of de novo models

Hao Fan, Xavier Periole, Alan E. Mark

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2012

Language:

english

File:

PDF, 1.14 MB

english, 2012

11

Molecular Dynamics Simulations of Transducin: Interdomain and Front to Back Communication in Activation and Nucleotide Exchange

Marc A. Ceruso, Xavier Periole, Harel Weinstein

Journal:

Journal of Molecular Biology

Year:

2004

Language:

english

File:

PDF, 2.09 MB

english, 2004

12

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

13

Dimerization of Amino Acid Side Chains: Lessons from the Comparison of Different Force Fields

de Jong, Djurre H., Periole, Xavier, Marrink, Siewert J.

Journal:

Journal of Chemical Theory and Computation

Year:

2012

Language:

english

File:

PDF, 3.94 MB

english, 2012

14

Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations

Bulacu, Monica, Goga, Nicolae, Zhao, Wei, Rossi, Giulia, Monticelli, Luca, Periole, Xavier, Tieleman, D. Peter, Marrink, Siewert J.

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 1.22 MB

english, 2013

15

The power of coarse graining in biomolecular simulations

Ingólfsson, Helgi I., Lopez, Cesar A., Uusitalo, Jaakko J., de Jong, Djurre H., Gopal, Srinivasa M., Periole, Xavier, Marrink, Siewert J.

Journal:

Wiley Interdisciplinary Reviews: Computational Molecular Science

Year:

2014

Language:

english

File:

PDF, 1.55 MB

english, 2014

16

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

17

Structural Determinants of the Supramolecular Organization of G Protein-Coupled Receptors in Bilayers

Periole, Xavier, Knepp, Adam M., Sakmar, Thomas P., Marrink, Siewert J., Huber, Thomas

Journal:

Journal of the American Chemical Society

Year:

2012

Language:

english

File:

PDF, 1.60 MB

english, 2012

18

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

19

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

20

Announcement

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

Journal:

Schizophrenia Research

Year:

1993

File:

PDF, 30 KB

1993

21

Biochemical Crosslinking and Liquid Chromatography-Mass Spectrometry Demonstrate a Rhodopsin Dimerization Interface Mediated by Helices 1 and 8

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

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 40 KB

english, 2012

22

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

23

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

24

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

25

Aggregation States Driven by Dipole Interactions Regulates Action Mechanism of Polyene Antibiotics

Carrillo-Tripp, Mauricio, Periole, Xavier, García-González, Acione, Espinosa-Caballero, Marcel, Vargas-González, Cristina, de Vries, Alex H., Ortega-Blake, Iván

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 34 KB

english, 2013

26

Supramolecular Organization of Rod Outer Segment Membrane: New Rhodopsin Dimer Interface and Insights from the β2Ar-Gs Complex

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

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 60 KB

english, 2014

27

Simulation of Photosystem Ii Dynamics in the Thylakoid Membrane

van Eerden, Floris J., de Jong, Djurre H., Periole, Xavier, Marrink, Siewert-Jan

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 83 KB

english, 2014

28

Amphotericin B Versus a Reduced Toxicity Chemical Analog in Aqueous and Lipid Media: An Md Comparative Study

Espinosa-Caballero, Marcel I., Periole, Xavier, de Vries, Alex, Vargas-González, M. Cristina, Marrink, Siewert J., Ortega-Blake, Iván, Carrillo-Tripp, Mauricio

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 40 KB

english, 2014

29

Factors That Affect the Degree of Twist in β-Sheet Structures: A Molecular Dynamics Simulation Study of a Cross-β Filament of the GNNQQNY Peptide

Periole, Xavier, Rampioni, Aldo, Vendruscolo, Michele, Mark, Alan E.

Journal:

Journal of Physical Chemistry B

Year:

2009

Language:

english

File:

PDF, 2.46 MB

english, 2009

30

Factors That Affect the Degree of Twist in β-Sheet Structures: A Molecular Dynamics Simulation Study of a Cross-β Filament of the GNNQQNY Peptide

Periole, Xavier, Rampioni, Aldo, Vendruscolo, Michele, Mark, Alan E.

Journal:

Journal of Physical Chemistry B

Year:

2009

Language:

english

File:

PDF, 40 KB

english, 2009

31

Lipid Organization of the Plasma Membrane

Ingólfsson, Helgi I., Melo, Manuel N., van Eerden, Floris J., Arnarez, Clément, Lopez, Cesar A., Wassenaar, Tsjerk A., Periole, Xavier, de Vries, Alex H., Tieleman, D. Peter, Marrink, Siewert J.

Journal:

Journal of the American Chemical Society

Year:

2014

Language:

english

File:

PDF, 8.57 MB

english, 2014

32

Phytochemicals Perturb Membranes and Promiscuously Alter Protein Function

Ingólfsson, Helgi I., Thakur, Pratima, Herold, Karl F., Hobart, E. Ashley, Ramsey, Nicole B., Periole, Xavier, de Jong, Djurre H., Zwama, Martijn, Yilmaz, Duygu, Hall, Katherine, Maretzky, Thorsten, H

Journal:

ACS Chemical Biology

Year:

2014

Language:

english

File:

PDF, 4.14 MB

english, 2014

33

Acid−Base Equilibria in Rhodopsin: Dependence of the Protonation State of Glu134 on Its Environment †

Periole, Xavier, Ceruso, Marc A., Mehler, Ernest L.

Journal:

Year:

2004

Language:

english

File:

PDF, 117 KB

english, 2004

34

Rhodopsin Forms a Dimer with Cytoplasmic Helix 8 Contacts in Native Membranes

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

Journal:

Year:

2012

Language:

english

File:

PDF, 1.20 MB

english, 2012

35

Evidence for Cardiolipin Binding Sites on the Membrane-Exposed Surface of the Cytochrome bc 1

Arnarez, Clement, Mazat, Jean-Pierre, Elezgaray, Juan, Marrink, Siewert-J, Periole, Xavier

Journal:

Journal of the American Chemical Society

Year:

2013

Language:

english

File:

PDF, 1.21 MB

english, 2013

36

Protofibrillar Assembly Toward the Formation of Amyloid Fibrils

Sørensen, Jesper, Periole, Xavier, Skeby, Katrine K., Marrink, Siewert-J., Schiøtt, Birgit

Journal:

The Journal of Physical Chemistry Letters

Year:

2011

Language:

english

File:

PDF, 3.21 MB

english, 2011

37

Comment on “On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models” by M. Winger, D. Trzesniak, R. Baron and W. F. van Gunsteren, Phys. Chem. Chem. Phys., 2009, 11, 1934

Marrink, Siewert J., Periole, Xavier, Tieleman, D. Peter, de Vries, Alex H.

Journal:

Physical Chemistry Chemical Physics

Year:

2010

Language:

english

File:

PDF, 120 KB

english, 2010

38

Dry Martini, a Coarse-Grained Force Field for Lipid Membrane Simulations with Implicit Solvent

Arnarez, Clément, Uusitalo, Jaakko J., Masman, Marcelo F., Ingólfsson, Helgi I., de Jong, Djurre H., Melo, Manuel N., Periole, Xavier, de Vries, Alex H., Marrink, Siewert J.

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 20.20 MB

english, 2015

39

Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent

Periole, Xavier, Mark, Alan E.

Journal:

The Journal of Chemical Physics

Year:

2007

Language:

english

File:

PDF, 1.09 MB

english, 2007

40

Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex

de Jong, Djurre H., Liguori, Nicoletta, van den Berg, Tom, Arnarez, Clement, Periole, Xavier, Marrink, Siewert J.

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 8.96 MB

english, 2015

41

Correction to “Atomistic and Coarse Grain Topologies for the Cofactors Associated with the PhotoSystem II Core Complex”

de Jong, Djurre H., Liguori, Nicoletta, van den Berg, Tom, Arnarez, Clement, Periole, Xavier, Marrink, Siewert J.

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 107 KB

english, 2015

42

Molecular mechanism of cardiolipin-mediated assembly of respiratory chain supercomplexes

Arnarez, Clement, Marrink, Siewert J., Periole, Xavier

Journal:

Chemical Science

Year:

2016

File:

PDF, 2.63 MB

2016

43

Molecular mechanism of cardiolipin-mediated assembly of respiratory chain supercomplexes

Arnarez, Clement, Marrink, Siewert J., Periole, Xavier

Journal:

Chemical Science

Year:

2016

Language:

english

File:

PDF, 2.63 MB

english, 2016

44

In Silico Modeling of Biologically Complex Membranes

Ingolfsson, Helgi I., Melo, Manuel N., Baoukina, Svetlana, Wassenaar, Tsjerk A., Periole, Xavier, de Vries, Alex H., Tieleman, D. Peter, Marrink, Siewert J.

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 45 KB

english, 2016

45

Computational Lipidomics and the Lipid Organization of Cell Envelopes

Ingolfsson, Helgi I., Melo, Manuel N., Wassenaar, Tsjerk A., Periole, Xavier, de Vries, Alex H., Tieleman, D. Peter, Marrink, Siewert J.

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 47 KB

english, 2015

46

The Role of Protein Conformational Changes in Tuning the Fluorescence State of Light-Harvesting Complexes

Liguori, Nicoletta, Periole, Xavier, Roy, Laura M., Bot, Yarah, Marrink, Siewert J., Croce, Roberta

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 43 KB

english, 2016

47

Molecular Dynamics of Photosystem II Embedded in the Thylakoid Membrane

van Eerden, Floris J., van den Berg, Tom, Frederix, Pim Wilhelmus Johannes Maria, de Jong, Djurre H., Periole, Xavier, Marrink, Siewert J.

Journal:

Journal of Physical Chemistry B

Year:

2016

Language:

english

File:

PDF, 30.90 MB

english, 2016

48

From light-harvesting to photoprotection: structural basis of the dynamic switch of the major antenna complex of plants (LHCII)

Liguori, Nicoletta, Periole, Xavier, Marrink, Siewert J., Croce, Roberta

Journal:

Scientific Reports

Year:

2015

Language:

english

File:

PDF, 1.60 MB

english, 2015

49

Mapping Cholesterol Binding Sites on the Human Dopamine Transporter

Zeppelin, Talia, Periole, Xavier, Schiøtt, Birgit

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 46 KB

english, 2017

50

Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex

Van Eerden, Floris J., Melo, Manuel N., Frederix, Pim W. J. M., Periole, Xavier, Marrink, Siewert J.

Journal:

Nature Communications

Year:

2017

Language:

english

File:

PDF, 2.57 MB

english, 2017

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