X. Periole

发表

The MARTINI Coarse-Grained Force Field: Extension to Proteins.

R. Larson, D. Tieleman, S. Marrink, 2008, Journal of chemical theory and computation.

Lipid organization of the plasma membrane.

Helgi I Ingólfsson, Helgi I. Ingólfsson, Siewert J Marrink, 2014, Journal of the American Chemical Society.

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

Xavier Periole, Siewert-Jan Marrink, M. Ceruso, 2009, Journal of chemical theory and computation.

Improved Parameters for the Martini Coarse-Grained Protein Force Field.

W F Drew Bennett, Siewert J Marrink, Tsjerk A Wassenaar, 2013, Journal of chemical theory and computation.

Identification of cardiolipin binding sites on cytochrome c oxidase at the entrance of proton channels

S. Marrink, X. Periole, C. Arnarez, 2013, Scientific Reports.

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

B. Honig, Hao Fan, A. Mark, 2008, Proteins.

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

Hao Fan, A. Mark, X. Periole, 2012, Proteins.

Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations.

D. Tieleman, S. Marrink, L. Monticelli, 2013, Journal of chemical theory and computation.

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

A. Mark, X. Periole, 2007, The Journal of chemical physics.

Computational ‘microscopy’ of cellular membranes

Helgi I Ingólfsson, Helgi I. Ingólfsson, Siewert J Marrink, 2016, Journal of Cell Science.

G protein-coupled receptors self-assemble in dynamics simulations of model bilayers.

Thomas Huber, Xavier Periole, Siewert-Jan Marrink, 2007, Journal of the American Chemical Society.

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

S. Marrink, X. Periole, D. H. de Jong, 2015, The journal of physical chemistry. B.

Effect of palmitoylation on the dimer formation of the human dopamine transporter

Nils A. Berglund, X. Periole, B. Schiøtt, 2021, Scientific Reports.

Dimer Interface of the Human Serotonin Transporter and Effect of the Membrane Composition

X. Periole, B. Schiøtt, T. Zeppelin, 2018, Scientific Reports.

Probing Self-Assembly of G Protein-Coupled Receptor Oligomers in Membranes Using Molecular Dynamics Modeling and Experimental Approaches

T. Huber, T. Sakmar, X. Periole, 2017 .

Chapter 20 The Martini Coarse-Grained Force Field

S. Marrink, X. Periole, 2012 .

Molecular dynamics simulations reveal that apo‐HisJ can sample a closed conformation

H. Vogel, X. Periole, B. Chu, 2014, Proteins.

The MARTINI force field

S. Marrink, H. Risselada, X. Periole, 2008 .

Energetics Underlying Twist Polymorphisms in Amyloid Fibrils.

S. Marrink, T. Huber, T. Sakmar, 2018, The journal of physical chemistry. B.

Cholesterol binding to a conserved site modulates the conformation, pharmacology, and transport kinetics of the human serotonin transporter

Louise Laursen, H. Müller, X. Periole, 2018, The Journal of Biological Chemistry.

Dry Martini, a coarse-grained force field for lipid membrane simulations with implicit solvent.

Helgi I Ingólfsson, Helgi I. Ingólfsson, Siewert J Marrink, 2015, Journal of chemical theory and computation.

Membrane Receptors & Signal Transduction I

M. Mofrad, W. Wall, M. Nugent, 2009 .

Martini 3: a general purpose force field for coarse-grained molecular dynamics

Bart M. H. Bruininks, Paulo C. T. Souza, N. Reuter, 2021, Nature Methods.

In silico design of robust bolalipid membranes.

Siewert J Marrink, S. Marrink, X. Periole, 2012, Biomacromolecules.

An Amphotericin B Derivative Equally Potent to Amphotericin B and with Increased Safety

Mauricio Carrillo-Tripp, Siewert J. Marrink, Xavier Periole, 2016, PloS one.

Phytochemicals Perturb Membranes and Promiscuously Alter Protein Function

Helgi I. Ingólfsson, Jon T. Sack, Katherine C. Hall, 2014, ACS chemical biology.

Structural determinants of the supramolecular organization of G protein-coupled receptors in bilayers.

Siewert J Marrink, Thomas Huber, Xavier Periole, 2012, Journal of the American Chemical Society.

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

Xavier Periole, X. Periole, 2017, Chemical reviews.

Key issues in the computational simulation of GPCR function: representation of loop domains

S. A. Hassan, Harel Weinstein, Ernest L. Mehler, 2002, J. Comput. Aided Mol. Des..

Molecular Modeling Investigation of the Interaction between Humicola insolens Cutinase and SDS Surfactant Suggests a Mechanism for Enzyme Inactivation

Leonardo De Maria, Lisbeth Ravnkilde Kjølbye, Birgit Schiøtt, 2019, J. Chem. Inf. Model..

Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex

Pim W. J. M. Frederix, S. Marrink, X. Periole, 2017, Nature Communications.

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

Alan E. Mark, Emanuele Paci, Xavier Periole, 2009, J. Comput. Chem..

Insight into the molecular mechanism behind PEG-mediated stabilization of biofluid lipases

B. Pérez, A. Perriman, X. Periole, 2018, Scientific Reports.

Dimer Interface of the Human Serotonin Transporter and Effect of the Membrane Composition

X. Periole, B. Schiøtt, T. Zeppelin, 2018, Scientific Reports.

Acid-base equilibria in rhodopsin: dependence of the protonation state of glu134 on its environment.

Xavier Periole, M. Ceruso, E. Mehler, 2004, Biochemistry.

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

S. Marrink, X. Periole, N. Liguori, 2015, Scientific Reports.

The power of coarse graining in biomolecular simulations

Helgi I Ingólfsson, Helgi I. Ingólfsson, Siewert J Marrink, 2013, Wiley interdisciplinary reviews. Computational molecular science.

Molecular dynamics simulations of transducin: interdomain and front to back communication in activation and nucleotide exchange.

H. Weinstein, M. Ceruso, X. Periole, 2004, Journal of molecular biology.

The Martini coarse-grained force field.

Xavier Periole, Siewert-Jan Marrink, S. Marrink, 2013, Methods in molecular biology.

Molecular mechanism of cardiolipin-mediated assembly of respiratory chain supercomplexes

S. Marrink, X. Periole, C. Arnarez, 2016, Chemical science.

Molecular Dynamics of Photosystem II Embedded in the Thylakoid Membrane.

Siewert J Marrink, Tom van den Berg, Xavier Periole, 2017, The journal of physical chemistry. B.

Evidence for cardiolipin binding sites on the membrane-exposed surface of the cytochrome bc1.

Jean-Pierre Mazat, Juan Elezgaray, Xavier Periole, 2013, Journal of the American Chemical Society.

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

M. Vendruscolo, X. Periole, A. E. Mark, 2007, Proteins.

A direct interaction of cholesterol with the dopamine transporter prevents its out-to-inward transition

Birgit Schiøtt, Xavier Periole, Steffen Sinning, 2018, PLoS Comput. Biol..

Insight into the molecular mechanism behind PEG-mediated stabilization of biofluid lipases

R. Sessions, B. Pérez, Zheng Guo, 2018, Scientific Reports.

Factors that affect the degree of twist in beta-sheet structures: a molecular dynamics simulation study of a cross-beta filament of the GNNQQNY peptide.

A. Mark, M. Vendruscolo, X. Periole, 2009, The journal of physical chemistry. B.

Rhodopsin forms a dimer with cytoplasmic helix 8 contacts in native membranes.

Thomas Huber, Xavier Periole, Siewert-Jan Marrink, 2012, Biochemistry.

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.

Siewert J Marrink, D Peter Tieleman, Xavier Periole, 2010, Physical chemistry chemical physics : PCCP.

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

Siewert J Marrink, Xavier Periole, Djurre H de Jong, 2012, Journal of chemical theory and computation.

ERRATUM: Identification of cardiolipin binding sites on cytochrome c oxidase at the entrance of proton channels

S. Marrink, X. Periole, C. Arnarez, 2013, Scientific Reports.

DNA-Encircled Lipid Bilayers

T. Huber, K. Fahmy, M. Matthies, 2018, bioRxiv.

DNA-Encircled Lipid Bilayers

T. Huber, K. Fahmy, M. Matthies, 2018, bioRxiv.

Protofibrillar Assembly Toward the Formation of Amyloid Fibrils

Birgit Schiøtt, Katrine Kirkeby Skeby, Siewert J. Marrink, 2011 .

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

M. Ceruso, S. Marrink, X. Periole, 2009, Journal of chemical theory and computation.

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

A. Mark, X. Periole, 2007, The Journal of chemical physics.

Computational ‘microscopy’ of cellular membranes

Helgi I. Ingólfsson, S. Marrink, X. Periole, 2016, Journal of Cell Science.

New Effective Potentials Extraction Method for the Interaction between Cations and Water

Y. Sanejouand, X. Periole, I. Ortega‐Blake, 1998 .

Simple Two-Body Cation−Water Interaction Potentials Derived from ab Initio Calculations. Comparison to Results Obtained with an Empirical Approach

Y. Sanejouand, X. Periole, J. Daudey, 1997 .