Search filters

Authors whose works are in public domain in at least one jurisdiction

List of works by Siewert J Marrink

3D pressure field in lipid membranes and membrane-protein complexes.

scientific article published on 19 February 2009

A Multi-Scale Approach to Membrane Remodeling Processes

scientific article published on 23 July 2019

A Practical View of the Martini Force Field

scientific article published on 01 January 2019

A coarse-grained model for polyethylene oxide and polyethylene glycol: conformation and hydrodynamics.

scientific article

A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems ⬇️

scientific article published on November 21, 1997

A molecular view on the escape of lipoplexed DNA from the endosome

scientific article published on 16 April 2020

A single bicontinuous cubic phase induced by fusion peptides

scientific article published on 01 July 2009

A structural view onto disease-linked mutations in the human neutral amino acid exchanger ASCT1

scientific article published on 17 September 2021

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

scientific article published on July 1, 2011

Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength

scientific article published on 10 January 2019

Adaptive Resolution Simulation of MARTINI Solvents

scientific article published on 06 May 2014

Adaptive Resolution Simulation of Supramolecular Water: The Concurrent Making, Breaking, and Remaking of Water Bundles

scientific article published on 13 July 2016

Adaptive resolution simulation of an atomistic protein in MARTINI water

scientific article published on 01 February 2014

Adaptive resolution simulation of polarizable supramolecular coarse-grained water models

article

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

scientific article published on February 1, 1998

Alcohol Interactions with Lipid Bilayers.

scientific article published on 28 November 2017

Altered secondary structure of Dynorphin A associates with loss of opioid signalling and NMDA-mediated excitotoxicity in SCA23.

scientific article

Amylose folding under the influence of lipids.

scientific article published on 17 October 2012

An Allosteric Pathway in Copper, Zinc Superoxide Dismutase Unravels the Molecular Mechanism of the G93A Amyotrophic Lateral Sclerosis-Linked Mutation

scientific article published on 03 December 2019

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

scientific article

Anomalous viscosity effect in the early stages of the ion-assisted adhesion/fusion event between lipid bilayers: a theoretical and computational study.

scientific article published in June 2013

Antimicrobial peptides in action

scientific article published on 01 September 2006

Application of mean field boundary potentials in simulations of lipid vesicles

scientific article published on 30 May 2008

Association behaviour of glucitol amine gemini surfactants : Self-consistent-field theory and molecular-dynamics simulations

scientific article

Asymmetric CorA Gating Mechanism as Observed by Molecular Dynamics Simulations

scientific article published on 22 April 2021

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

scientific article published on 8 June 2015

Backmapping triangulated surfaces to coarse-grained membrane models

scientific article published on 08 May 2020

Benchmark of Schemes for Multiscale Molecular Dynamics Simulations.

scientific article published in April 2015

Binding of quinazolinones to c-KIT G-quadruplex; an interplay between hydrogen bonding and π-π stacking

scientific article published on 05 July 2019

Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations

scientific article

CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field

scientific article published on 27 August 2015

CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides

scientific article published on 3 August 2017

Capturing Choline-Aromatics Cation-π Interactions in the MARTINI Force Field

scientific article published on 09 March 2020

Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations

scientific article published on 24 June 2021

Caught in the Act: Mechanistic Insight into Supramolecular Polymerization-Driven Self-Replication from Real-Time Visualization

scientific article published on 31 July 2020

Ceramides bind VDAC2 to trigger mitochondrial apoptosis

scientific article published on 23 April 2019

Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations.

scientific article published on 5 March 2015

Charge-dependent interactions of monomeric and filamentous actin with lipid bilayers

scientific article published on 02 March 2020

Cholesterol Flip-Flop Impacts Domain Registration in Plasma Membrane Models

scientific article published on 11 September 2018

Cholesterol in bilayers with PUFA chains: doping with DMPC or POPC results in sterol reorientation and membrane-domain formation

scientific article published on September 2010

Cholesterol shows preference for the interior of polyunsaturated lipid membranes

scientific article published on 13 December 2007

Coarse-grain modelling of protein-protein interactions

scientific article

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

scientific article published on 19 August 2009

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

scientific article published on 27 January 2010

Comparison of Thermodynamic Properties of Coarse-Grained and Atomic-Level Simulation Models

scientific article published on 01 February 2007

Computational 'microscopy' of cellular membranes

scientific article

Computational Lipidomics of the Neuronal Plasma Membrane.

scientific article published on 4 November 2017

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations

scientific article published on 24 April 2015

Computational Modeling of Realistic Cell Membranes

scientific article published on 09 January 2019

Computational Redesign of an ω-Transaminase from <i>Pseudomonas jessenii</i> for Asymmetric Synthesis of Enantiopure Bulky Amines

scientific article published on 13 August 2021

Computational and Experimental Advances in Biomembranes: Resolving Their Complexity

scientific article published on 01 November 2020

Computational library design for increasing haloalkane dehalogenase stability

scientific article

Computational microscopy of cyclodextrin mediated cholesterol extraction from lipid model membranes ⬇️

scientific article published on January 1, 2013

Computationally designed libraries for rapid enzyme stabilization

scientific article

Computationally efficient and accurate enantioselectivity modeling by clusters of molecular dynamics simulations

scientific article published on 30 June 2014

Concerted diffusion of lipids in raft-like membranes.

scientific article

Coupled binding mechanism of three sodium ions and aspartate in the glutamate transporter homologue GltTk

scientific article published on 10 November 2016

Curvature effects on lipid packing and dynamics in liposomes revealed by coarse grained molecular dynamics simulations.

scientific article published on 29 January 2009

Curvature-dependent elastic properties of liquid-ordered domains result in inverted domain sorting on uniaxially compressed vesicles

scientific article published on 05 April 2011

Defined lipid analogues induce transient channels to facilitate drug-membrane traversal and circumvent cancer therapy resistance

scientific article published on January 2013

Design and Properties of Genetically Encoded Probes for Sensing Macromolecular Crowding

scientific article published in May 2017

Determining equilibrium constants for dimerization reactions from molecular dynamics simulations

scientific article published on 05 April 2011

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

scientific article published on 29 February 2012

Disaccharides impact the lateral organization of lipid membranes.

scientific article

Disturb or stabilize? A molecular dynamics study of the effects of resorcinolic lipids on phospholipid bilayers

scientific article published on April 2009

Does isoprene protect plant membranes from thermal shock? A molecular dynamics study

scientific article published on 04 October 2006

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

scientific article published on 17 December 2014

Dual Resolution Membrane Simulations Using Virtual Sites

scientific article published on 21 April 2020

Dual action of BPC194: a membrane active peptide killing bacterial cells

scientific article

Efficient Algorithms for Langevin and DPD Dynamics

scientific article published on 13 June 2012

Electrophoretic mobility does not always reflect the charge on an oil droplet

scientific article

Emerging Diversity in Lipid-Protein Interactions

scientific article published on 13 February 2019

Enantioselective enzymes by computational design and in silico screening

scientific article published on 4 February 2015

Energetics Underlying Twist Polymorphisms in Amyloid Fibrils

scientific article published on 19 December 2017

Enhancing Molecular n-Type Doping of Donor-Acceptor Copolymers by Tailoring Side Chains

scientific article published on 11 January 2018

Establishing conditions for simulating hydrophobic solutes in electric fields by molecular dynamics: effects of the long-range van der Waals treatment on the apparent particle mobility.

scientific article

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

scientific article published on 13 February 2013

Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex.

scientific article

Finite size scaling for percolation on elongated lattices in two and three dimensions

scientific article published in September 2000

Fluorinated Alcohols' Effects on Lipid Bilayer Properties

scientific article published on 01 August 2018

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

scientific article published on 23 October 2015

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

article

Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations

scientific article

Gangliosides Destabilize Lipid Phase Separation in Multicomponent Membranes

scientific article published on 06 September 2019

Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations

scientific article published on 23 February 2008

Gaussian curvature elasticity determined from global shape transformations and local stress distributions: a comparative study using the MARTINI model

scientific article published on 01 January 2013

Global structural changes of an ion channel during its gating are followed by ion mobility mass spectrometry

scientific article published on 17 November 2014

Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models.

scientific article published on 21 January 2014

Helfrich model of membrane bending: from Gibbs theory of liquid interfaces to membranes as thick anisotropic elastic layers.

scientific article published on 03 February 2014

High-Throughput Simulations Reveal Membrane-Mediated Effects of Alcohols on MscL Gating.

scientific article published on 26 January 2017

High-Throughput Simulations of Dimer and Trimer Assembly of Membrane Proteins. The DAFT Approach

scientific article published on 26 March 2015

Hsc70-4 Deforms Membranes to Promote Synaptic Protein Turnover by Endosomal Microautophagy.

scientific article published in November 2015

Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites

scientific article published on 15 April 2011

Hydrophobic compounds reshape membrane domains

scientific article (publication date: October 2014)

Immobilization of the plug domain inside the SecY channel allows unrestricted protein translocation.

scientific article published on 19 May 2010

Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations.

scientific article published on 16 July 2013

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

scientific article published on 28 November 2012

In SilicoStudy of Full-Length Amyloid β 1−42 Tri- and Penta-Oligomers in Solution

scientific article published on 01 August 2009

In silico design of robust bolalipid membranes

scientific article published on 01 December 2011

Influence of hydrophobic mismatch and amino acid composition on the lateral diffusion of transmembrane peptides

scientific article

Insight into the complete substrate-binding pocket of ThiT by chemical and genetic mutations

scientific article published on 31 March 2017

Intramolecular photostabilization via triplet-state quenching: design principles to make organic fluorophores "self-healing".

scientific article published on 9 October 2015

Ironing out their differences: dissecting the structural determinants of a phenylalanine aminomutase and ammonia lyase

scientific article

Lateral pressure profiles in lipid monolayers

scientific article published on 01 January 2010

Line-Tension Controlled Mechanism for Influenza Fusion ⬇️

scientific article published on June 28, 2012

Lipid Fingerprints and Cofactor Dynamics of Light-Harvesting Complex II in Different Membranes

scientific article published on 22 March 2019

Lipid acrobatics in the membrane fusion arena.

scientific article published on January 2011

Lipid and Peptide Diffusion in Bilayers: The Saffman-Delbrück Model and Periodic Boundary Conditions.

scientific article

Lipid organization of the plasma membrane

scientific article

Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes

scientific article

Lipid-Protein Interactions Are Unique Fingerprints for Membrane Proteins.

scientific article

Lipid-mediated interactions tune the association of glycophorin A helix and its disruptive mutants in membranes.

scientific article published on 23 August 2010

Lipids out of equilibrium: energetics of desorption and pore mediated flip-flop

scientific article published on 01 September 2006

Location, tilt, and binding: a molecular dynamics study of voltage-sensitive dyes in biomembranes.

scientific article published in December 2009

MARTINI Coarse-Grained Model for Crystalline Cellulose Microfibers

article

Martini Coarse-Grained Force Field: Extension to Carbohydrates.

scientific article

Martini Coarse-Grained Force Field: Extension to DNA.

scientific article

Martini Coarse-Grained Force Field: Extension to RNA.

scientific article published on 17 June 2017

Martini Force Field Parameters for Glycolipids.

scientific article

Mechanisms shaping cell membranes

scientific article

Mechanosensitive membrane channels in action

scientific article published on 11 January 2008

Membrane mediated toppling mechanism of the folate energy coupling factor transporter

scientific article published on 09 April 2020

Membrane poration by antimicrobial peptides combining atomistic and coarse-grained descriptions

scientific article published on 01 January 2010

Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations

article published in 2013

Molecular Dynamics of Photosystem II Embedded in the Thylakoid Membrane

scientific article

Molecular Dynamics of the Association of L-Selectin and FERM Regulated by PIP2.

scientific article published in April 2018

Molecular Mechanism of Lipid Nanodisk Formation by Styrene-Maleic Acid Copolymers

scientific article published on 20 June 2018

Molecular Structure of Membrane Tethers ⬇️

scientific article published on April 18, 2012

Molecular dynamics simulation of a lipid diamond cubic phase.

scientific article published in December 2001

Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles

scientific article published on 01 December 2003

Molecular dynamics simulation of the spontaneous formation of a small DPPC vesicle in water in atomistic detail

scientific article published on 01 April 2004

Molecular dynamics simulations in photosynthesis

scientific article published on 15 April 2020

Molecular dynamics simulations of mixed micelles modeling human bile.

scientific article published in April 2002

Molecular mechanism for bidirectional regulation of CD44 for lipid raft affiliation by palmitoylations and PIP2

scientific article published on 09 April 2020

Molecular mechanism of cardiolipin-mediated assembly of respiratory chain supercomplexes.

scientific article published on 15 March 2016

Molecular mechanism of cyclodextrin mediated cholesterol extraction

scientific article (publication date: March 2011)

Molecular plasticity regulates oligomerization and cytotoxicity of the multipeptide-length amyloid-β peptide pool

scientific article

Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments.

scientific article published on 24 April 2018

Molecular structure of the lecithin ripple phase

scientific article

Molecular versus excitonic disorder in individual artificial light-harvesting systems

scientific article published on 26 September 2020

Molecular view of cholesterol flip-flop and chemical potential in different membrane environments.

scientific article published in September 2009

Molecular view of the role of fusion peptides in promoting positive membrane curvature.

scientific article published on 10 January 2012

Multiscale Simulation of Protein Hydration Using the SWINGER Dynamical Clustering Algorithm.

scientific article published on 13 February 2018

N-type organic thermoelectrics: demonstration of ZT > 0.3.

scientific article published on 10 November 2020

Parameters for Martini sterols and hopanoids based on a virtual-site description

scientific article published on 01 December 2015

Partitioning of Lipids at Domain Boundaries in Model Membranes ⬇️

scientific article published on December 15, 2010

Perspective on the Martini model.

scientific article published on August 2013

Perspective: a stirring role for metabolism in cells

scientific article published in 2022

Phytochemicals perturb membranes and promiscuously alter protein function.

scientific article

Pitfalls of the Martini Model

scientific article published on 24 September 2019

Polarizable water model for the coarse-grained MARTINI force field

scientific article

Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials

scientific article published on 10 January 2022

Prediction of Thylakoid Lipid Binding Sites on Photosystem II.

scientific article published in December 2017

Pressure-area isotherm of a lipid monolayer from molecular dynamics simulations

scientific article published on 01 November 2007

Protein shape change has a major effect on the gating energy of a mechanosensitive channel

scientific article

Protein-ligand binding with the coarse-grained Martini model

scientific article published on 24 July 2020

Protocol for Simulations of PEGylated Proteins with Martini 3

scientific article published on 01 January 2021

Reconstruction of atomistic details from coarse-grained structures

scientific article published in April 2010

Release of content through mechano-sensitive gates in pressurized liposomes

scientific article

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

scientific article published on 27 February 2012

Role of Charge and Hydrophobicity in Liprotide Formation: A Molecular Dynamics Study with Experimental Constraints

scientific article published on 20 November 2017

Role of lipids in spheroidal high density lipoproteins

scientific article

SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids

scientific article published on 19 April 2019

Semiconducting single-walled carbon nanotubes on demand by polymer wrapping

article

Semiprocessive Hyperglycosylation of Adhesin by Bacterial Protein <i>N</i>-Glycosyltransferases

scientific article published on 05 January 2021

Sequential Voxel-Based Leaflet Segmentation of Complex Lipid Morphologies

scientific article published on 06 October 2021

Serine Phosphorylation of L-Selectin Regulates ERM Binding, Clustering, and Monocyte Protrusion in Transendothelial Migration

scientific article published on 25 September 2019

Simulation of MscL gating in a bilayer under stress.

scientific article published on April 2003

Simulation of domain formation in DLPC-DSPC mixed bilayers.

scientific article

Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model

scientific article published on 28 March 2005

Simulation of polyethylene glycol and calcium-mediated membrane fusion

scientific article published on 01 March 2014

Simulation of pore formation in lipid bilayers by mechanical stress and electric fields

scientific article

Simulation of the Spontaneous Aggregation of Phospholipids into Bilayers

scientific article published on 01 September 2001

Simulation studies of pore and domain formation in a phospholipid monolayer

scientific article published on 01 January 2005

Sphere-to-rod transitions of nonionic surfactant micelles in aqueous solution modeled by molecular dynamics simulations

scientific article published on 27 October 2011

Stability and dynamics of membrane-spanning DNA nanopores.

scientific article

Stability of asymmetric lipid bilayers assessed by molecular dynamics simulations

scientific article published in October 2009

Structural and Spectroscopic Properties of Assemblies of Self-Replicating Peptide Macrocycles.

scientific article published on 19 July 2017

Structural basis for the enhanced activity of cyclic antimicrobial peptides: the case of BPC194

scientific article published on 08 May 2011

Structural characterization of supramolecular hollow nanotubes with atomistic simulations and SAXS

scientific article published on 18 September 2020

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

scientific article

Structural insights into K48-linked ubiquitin chain formation by the Pex4p-Pex22p complex.

scientific article published on 27 December 2017

Structural investigation of MscL gating using experimental data and coarse grained MD simulations

scientific article

Synthetic Membrane Shaper for Controlled Liposome Deformation

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

scientific article published in May 2008

The MARTINI force field: coarse grained model for biomolecular simulations

scientific article (publication date: 12 July 2007)

The Martini Coarse-Grained Force Field ⬇️

scientific article published on January 1, 2013

The Mechanism of Vesicle Fusion as Revealed by Molecular Dynamics Simulations

article

The N-terminal amphipathic helix of Pex11p self-interacts to induce membrane remodelling during peroxisome fission

scientific article published in March 2018

The activation mode of the mechanosensitive ion channel, MscL, by lysophosphatidylcholine differs from tension-induced gating

scientific article

The effect of aliphatic alcohols on fluid bilayers in unilamellar DOPC vesicles — A small-angle neutron scattering and molecular dynamics study ⬇️

scientific article published on April 29, 2011

The molecular face of lipid rafts in model membranes.

scholarly article

The power of coarse graining in biomolecular simulations.

scientific article

The structural basis for peptide selection by the transport receptor OppA

scientific article

Titratable Martini model for constant pH simulations

scientific article published on 01 July 2020

Toroidal pores formed by antimicrobial peptides show significant disorder.

scientific article published on 18 June 2008

Transferable MARTINI Model of Poly(ethylene Oxide)

scientific article published on 13 July 2018

Transmembrane helices can induce domain formation in crowded model membranes

scientific article published on 22 August 2011

Two distinct anionic phospholipid-dependent events involved in SecA-mediated protein translocation

scientific article published on 05 August 2019

Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology

scientific article published on 22 October 2018

Unidirectional rotating molecular motors dynamically interact with adsorbed proteins to direct the fate of mesenchymal stem cells

scientific article published on 29 January 2020

Vibrational Spectra of a Mechanosensitive Channel.

scientific article

cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations

scientific article published on 13 July 2017

Paulina is supported by:

About Paulina

Help