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Pitfalls of the Martini Model
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/jcc.20090openalex-snapshot
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6
inferredcites →https://doi.org/10.1002/jcc.540130812openalex-snapshot
THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method
inferredcites →https://doi.org/10.1002/jps.21494openalex-snapshot
Calculation of Molecular Lipophilicity: State-of-the-Art and Comparison of LogP Methods on more than 96,000 Compounds
inferredcites →https://doi.org/10.1002/wcms.1169openalex-snapshot
The power of coarse graining in biomolecular simulations
inferredcites →https://doi.org/10.1007/978-1-4939-9608-7_5openalex-snapshot
A Practical View of the Martini Force Field
inferredcites →https://doi.org/10.1007/978-94-015-7658-1_21openalex-snapshot
Interaction Models for Water in Relation to Protein Hydration
inferredcites →https://doi.org/10.1007/s10822-017-0059-9openalex-snapshot
Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models
inferredcites →https://doi.org/10.1007/s11120-020-00741-yopenalex-snapshot
Molecular dynamics simulations in photosynthesis
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Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations
inferredcites →https://doi.org/10.1016/0021-9991(77)90121-8openalex-snapshot
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
inferredcites →https://doi.org/10.1016/bs.pmbts.2020.01.001openalex-snapshot
Computer simulations of protein–membrane systems
inferredcites →https://doi.org/10.1016/j.bpj.2017.05.043openalex-snapshot
Martini Coarse-Grained Force Field: Extension to RNA
inferredcites →https://doi.org/10.1016/j.bpj.2019.03.009openalex-snapshot
Lipid Fingerprints and Cofactor Dynamics of Light-Harvesting Complex II in Different Membranes
inferredcites →https://doi.org/10.1016/j.cpc.2015.09.014openalex-snapshot
Martini straight: Boosting performance using a shorter cutoff and GPUs
inferredcites →https://doi.org/10.1016/j.sbi.2018.11.005openalex-snapshot
Advances in coarse-grained modeling of macromolecular complexes
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GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
inferredcites →https://doi.org/10.1021/acs.chemrev.8b00460openalex-snapshot
Computational Modeling of Realistic Cell Membranes
inferredcites →https://doi.org/10.1021/acs.chemrev.8b00538openalex-snapshot
Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance
inferredcites →https://doi.org/10.1021/acs.jctc.0c00056openalex-snapshot
Coarse-Grained Molecular Model for the Glycosylphosphatidylinositol Anchor with and without Protein
inferredcites →https://doi.org/10.1021/acs.jctc.5b00056openalex-snapshot
Automated Parametrization of the Coarse-Grained Martini Force Field for Small Organic Molecules
inferredcites →https://doi.org/10.1021/acs.jctc.5b00209openalex-snapshot
Computational Lipidomics with insane : A Versatile Tool for Generating Custom Membranes for Molecular Simulations
inferredcites →https://doi.org/10.1021/acs.jctc.5b00286openalex-snapshot
Martini Coarse-Grained Force Field: Extension to DNA
inferredcites →https://doi.org/10.1021/acs.jctc.6b00986openalex-snapshot
Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins
inferredcites →https://doi.org/10.1021/acs.jctc.7b00374openalex-snapshot
Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides
inferredcites →https://doi.org/10.1021/acs.jctc.9b00473openalex-snapshot
Pitfalls of the Martini Model
inferredcites →https://doi.org/10.1021/acs.jpcb.8b04760openalex-snapshot
Transferable MARTINI Model of Poly(ethylene Oxide)
inferredcites →https://doi.org/10.1021/acsaem.9b00307openalex-snapshot
Computational Microscopy of PEDOT:PSS/Cellulose Composite Paper
inferredcites →https://doi.org/10.1021/acscentsci.9b00084openalex-snapshot
Self-Assembly of Charge-Containing Copolymers at the Liquid–Liquid Interface
inferredcites →https://doi.org/10.1021/acsnano.6b07628openalex-snapshot
From Cooperative Self-Assembly to Water-Soluble Supramolecular Polymers Using Coarse-Grained Simulations
inferredcites →https://doi.org/10.1021/ci400112kopenalex-snapshot
Structural Determinants of Drug Partitioning in n-Hexadecane/Water System
inferredcites →https://doi.org/10.1021/ct200196mopenalex-snapshot
An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0
inferredcites →https://doi.org/10.1021/ct300646gopenalex-snapshot
Improved Parameters for the Martini Coarse-Grained Protein Force Field
inferredcites →https://doi.org/10.1021/ct400008popenalex-snapshot
Toward Optimized Potential Functions for Protein–Protein Interactions in Aqueous Solutions: Osmotic Second Virial Coefficient Calculations Using the MARTINI Coarse-Grained Force Field
inferredcites →https://doi.org/10.1021/ct9002114openalex-snapshot
Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition
inferredcites →https://doi.org/10.1021/ja9621760openalex-snapshot
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
inferredcites →https://doi.org/10.1021/jacs.6b11717openalex-snapshot
Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations
inferredcites →https://doi.org/10.1021/jp036508gopenalex-snapshot
Coarse Grained Model for Semiquantitative Lipid Simulations
inferredcites →https://doi.org/10.1021/jp071097fopenalex-snapshot
The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations
inferredcites →https://doi.org/10.1021/jp980017sopenalex-snapshot
Refinement and Parametrization of COSMO-RS
inferredcites →https://doi.org/10.1038/72430openalex-snapshot
Interhelical hydrogen bonding drives strong interactions in membrane proteins.
inferredcites →https://doi.org/10.1038/s41467-020-15554-9openalex-snapshot
Membrane mediated toppling mechanism of the folate energy coupling factor transporter
inferredcites →https://doi.org/10.1038/s41598-018-22912-7openalex-snapshot
Dimer Interface of the Human Serotonin Transporter and Effect of the Membrane Composition
inferredcites →https://doi.org/10.1039/c0sm00481bopenalex-snapshot
Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case
inferredcites →https://doi.org/10.1039/c2sm27201fopenalex-snapshot
Systematic coarse-graining methods for soft matter simulations – a review
inferredcites →https://doi.org/10.1039/c7ta06609kopenalex-snapshot
Enhancing doping efficiency by improving host-dopant miscibility for fullerene-based n-type thermoelectrics
inferredcites →https://doi.org/10.1039/c8cp02902dopenalex-snapshot
Morphology and ion diffusion in PEDOT:Tos. A coarse grained molecular dynamics simulation
inferredcites →https://doi.org/10.1039/c8cs00040aopenalex-snapshot
Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments
inferredcites →https://doi.org/10.1063/1.2408420openalex-snapshot
Canonical sampling through velocity rescaling
inferredcites →https://doi.org/10.1063/1.2978177openalex-snapshot
Statistically optimal analysis of samples from multiple equilibrium states
inferredcites →https://doi.org/10.1063/1.328693openalex-snapshot
Polymorphic transitions in single crystals: A new molecular dynamics method
inferredcites →https://doi.org/10.1063/1.445869openalex-snapshot
Comparison of simple potential functions for simulating liquid water
inferredcites →https://doi.org/10.1063/1.4818908openalex-snapshot
Perspective: Coarse-grained models for biomolecular systems
inferredcites →https://doi.org/10.1063/1.4937783openalex-snapshot
Parameters for Martini sterols and hopanoids based on a virtual-site description
inferredcites →https://doi.org/10.1063/1.4937805openalex-snapshot
Coarse-grained simulations of polyelectrolyte complexes: MARTINI models for poly(styrene sulfonate) and poly(diallyldimethylammonium)
inferredcites →https://doi.org/10.1073/pnas.041593698openalex-snapshot
Polar residues drive association of polyleucine transmembrane helices
inferredcites →https://doi.org/10.1073/pnas.0807527105openalex-snapshot
The molecular face of lipid rafts in model membranes
inferredcites →https://doi.org/10.1080/00268978400101201openalex-snapshot
A molecular dynamics method for simulations in the canonical ensemble
inferredcites →https://doi.org/10.1103/physreva.31.1695openalex-snapshot
Canonical dynamics: Equilibrium phase-space distributions
inferredcites →https://doi.org/10.1126/sciadv.aay5736openalex-snapshot
Multiple lipid binding sites determine the affinity of PH domains for phosphoinositide-containing membranes
inferredcites →https://doi.org/10.1126/science.1157834openalex-snapshot
Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems
inferredcites →https://doi.org/10.1201/9781420059564openalex-snapshot
Coarse-Graining of Condensed Phase and Biomolecular Systems
inferredcites →https://doi.org/10.1201/9781420059564.ch25openalex-snapshot
Structure-Based Coarse- and Fine-Graining in Soft Matter Simulations
inferredcites →https://doi.org/10.1371/journal.pcbi.1003638openalex-snapshot
Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?
inferredcites →https://doi.org/10.1371/journal.pone.0187936openalex-snapshot
Excessive aggregation of membrane proteins in the Martini model
inferredcites →https://doi.org/10.15698/cst2017.11.111openalex-snapshot
The role of hydrophobic matching on transmembrane helix packing in cells
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Resolving Donor–Acceptor Interfaces and Charge Carrier Energy Levels of Organic Semiconductors with Polar Side Chains
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The Martini Model in Materials Science
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Martini 3 Coarse‐Grained Force Field: Small Molecules
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Molecular dynamics insights on temperature and pressure effects on electroporation
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Assessing the Martini 3 protein model: A review of its path and potential
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Cholesterol plays a decisive role in tetraspanin assemblies during bilayer deformations
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Development of polarizable and hydration-focused water models for the Martini 3 force field
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Room for improvement in the initial martini 3 parameterization of peptide interactions
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Using coarse-grained models to examine structure-property relationships of diblock-arm star polymers
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Depletion of membrane cholesterol modifies structure, dynamic and activation of Nav1.7
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Cholesterol-induced suppression of Kir2 channels is mediated by decoupling at the inter-subunit interfaces
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Activity modulation of the Escherichia coli F1FO ATP synthase by a designed antimicrobial peptide via cardiolipin sequestering
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Recovery from desensitization in GluA2 AMPA receptors is affected by a single mutation in the N-terminal domain interface
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The nanotube express: Delivering a stapled peptide to the cell surface
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Benchmarking a dual-scale hybrid simulation framework for small globular proteins combining the CHARMM36 and Martini2 models
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How antimicrobial peptide indolicidin and its derivatives interact with phospholipid membranes: Molecular dynamics simulation
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Towards design of drugs and delivery systems with the Martini coarse-grained model
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Review: Towards design of drugs and delivery systems with the Martini coarse-grained model — R0/PR2
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Review: Towards design of drugs and delivery systems with the Martini coarse-grained model — R0/PR3
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Recommendation: Towards design of drugs and delivery systems with the Martini coarse-grained model — R0/PR4
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Recommendation: Towards design of drugs and delivery systems with the Martini coarse-grained model — R1/PR5
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Short Peptide Self-Assembly in the Martini Coarse-Grain Force Field Family
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Myomerger Induces Membrane Hemifusion and Regulates Fusion Pore Expansion
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Extending the Martini Coarse-Grained Force Field to N ‑Glycans
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Coarse-Grained Parameterization of Nucleotide Cofactors and Metabolites: Protonation Constants, Partition Coefficients, and Model Topologies
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Recent Open Issues in Coarse Grained Force Fields
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General Protocol for Constructing Molecular Models of Nanodiscs
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Modeling the Effect of Hydrophobicity on the Passive Permeation of Solutes across a Bacterial Model Membrane
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Improved Protein Dynamics and Hydration in the Martini3 Coarse-Grain Model
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Martini Mapper: An Automated Fragment-Based Mapping Algorithm for Developing Coarse-Grained Models within the Martini 3 Framework
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Lipopolysaccharide–Phospholipid Separation in the Outer Membrane Vesicle Model Promotes Preferential Binding of Antimicrobial Peptides at Lipid Interfaces
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Constrained Low-Dimensional Parametrization of Coarse-Grained Force Fields for Structural and Thermodynamic Consistency
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Intricate Role of Cholesterol in Membrane Fusion
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Fast-Forward: Automatic Assignment and Assessment of Bonded Parameters for the Martini Force Field
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Coarse-Grained Molecular Model for the Glycosylphosphatidylinositol Anchor with and without Protein
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Coupling Coarse-Grained to Fine-Grained Models via Hamiltonian Replica Exchange
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Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments
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Coarse-Grained Force Fields from the Perspective of Statistical Mechanics: Better Understanding of the Origins of a MARTINI Hangover
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The Synaptotagmin-1 C2B Domain Is a Key Regulator in the Stabilization of the Fusion Pore
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Bacterial Analogs to Cholesterol Affect Dimerization of Proteorhodopsin and Modulates Preferred Dimer Interface
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Simulations of the Upper Critical Solution Temperature Behavior of Poly(ornithine-co-citrulline)s Using MARTINI-Based Coarse-Grained Force Fields
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Automated Coarse-Grained Mapping Algorithm for the Martini Force Field and Benchmarks for Membrane–Water Partitioning
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c00615openalex-snapshot
Improved Parameterization of Phosphatidylinositide Lipid Headgroups for the Martini 3 Coarse-Grain Force Field
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Improving Martini 3 for Disordered and Multidomain Proteins
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Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework
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Accurate and Efficient Estimation of Lennard–Jones Interactions for Coarse-Grained Particles via a Potential Matching Method
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Extending the Martini 3 Coarse-Grained Force Field to Carbohydrates
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Bottom-up Coarse-Graining: Principles and Perspectives
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Martini 3 Coarse-Grained Force Field for Carbohydrates
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Scaling Protein–Water Interactions in the Martini 3 Coarse-Grained Force Field to Simulate Transmembrane Helix Dimers in Different Lipid Environments
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Machine Learning-Driven Multiscale Modeling: Bridging the Scales with a Next-Generation Simulation Infrastructure
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Effective Molecular Dynamics from Neural Network-Based Structure Prediction Models
inferred← citeshttps://doi.org/10.1021/acs.jctc.2c01029openalex-snapshot
NanoModeler CG: A Tool for Modeling and Engineering Functional Nanoparticles at a Coarse-Grained Resolution
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00471openalex-snapshot
Martini-3 Coarse-Grained Models for the Bacterial Lipopolysaccharide Outer Membrane of Escherichia coli
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00547openalex-snapshot
Martini 3 Coarse-Grained Force Field for Cholesterol
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00637openalex-snapshot
CGCompiler: Automated Coarse-Grained Molecule Parametrization via Noise-Resistant Mixed-Variable Optimization
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00641openalex-snapshot
Perspectives on Ligand/Protein Binding Kinetics Simulations: Force Fields, Machine Learning, Sampling, and User-Friendliness
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00874openalex-snapshot
When Data Are Lacking: Physics-Based Inverse Design of Biopolymers Interacting with Complex, Fluid Phases
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c01088openalex-snapshot
Coarse-Grained Model of Glycosaminoglycans for Biomolecular Simulations
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c01155openalex-snapshot
Exploring Free Energies of Specific Protein Conformations Using the Martini Force Field
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00645openalex-snapshot
Recalibration of MARTINI-3 Parameters for Improved Interactions between Peripheral Proteins and Lipid Bilayers
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00804openalex-snapshot
Chemically Transferable Electronic Coarse Graining for Polythiophenes
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c01026openalex-snapshot
The Role of Cholesterol in M2 Clustering and Viral Budding Explained
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c01466openalex-snapshot
A Neural-Network-Based Mapping and Optimization Framework for High-Precision Coarse-Grained Simulation
inferred← citeshttps://doi.org/10.1021/acs.jctc.5c00016openalex-snapshot
Kinetics and Mechanism of Phase Separation in Ternary Lipid Mixtures Containing APP C99: Atomistic vs Coarse-Grained MD Simulations
inferred← citeshttps://doi.org/10.1021/acs.jctc.5c00580openalex-snapshot
Data-Driven Coarse-Graining with Simple Functional Forms
inferred← citeshttps://doi.org/10.1021/acs.jctc.5c01178openalex-snapshot
Fast Parametrization of Martini3 Models for Fragments and Small Molecules
inferred← citeshttps://doi.org/10.1021/acs.jctc.5c01655openalex-snapshot
A Coarse-Grained MARTINI Model for Mucins
inferred← citeshttps://doi.org/10.1021/acs.jpcb.0c07212openalex-snapshot
Cationic Antiseptics Facilitate Pore Formation in Model Bacterial Membranes
inferred← citeshttps://doi.org/10.1021/acs.jpcb.0c09749openalex-snapshot
Coarse-Graining Organic Semiconductors: The Path to Multiscale Design
inferred← citeshttps://doi.org/10.1021/acs.jpcb.0c10992openalex-snapshot
Thermodynamics and Free Energy Landscape of BAR-Domain Dimerization from Molecular Simulations
inferred← citeshttps://doi.org/10.1021/acs.jpcb.1c03277openalex-snapshot
Evaluating Coarse-Grained MARTINI Force-Fields for Capturing the Ripple Phase of Lipid Membranes
inferred← citeshttps://doi.org/10.1021/acs.jpcb.2c00239openalex-snapshot
Coarse-Grained Simulations Suggest Potential Competing Roles of Phosphoinositides and Amphipathic Helix Structures in Membrane Curvature Sensing of the AP180 N-Terminal Homology Domain
inferred← citeshttps://doi.org/10.1021/acs.jpcb.3c01053openalex-snapshot
Investigating the Impact of the Glycolipid Content on Aurein 1.2 Pores in Prokaryotic Model Bilayers: A Coarse-Grain Molecular Dynamics Simulation Study
inferred← citeshttps://doi.org/10.1021/acs.jpcb.3c04843openalex-snapshot
Adaptive Sampling Methods for Molecular Dynamics in the Era of Machine Learning
inferred← citeshttps://doi.org/10.1021/acs.jpcb.3c05930openalex-snapshot
Palmitoylation of the Glucagon-like Peptide-1 Receptor Modulates Cholesterol Interactions at the Receptor–Lipid Microenvironment
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c02700openalex-snapshot
Ebola Virus Matrix Protein VP40 Single Mutations G198R and G201R Significantly Enhance Plasma Membrane Localization
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c03242openalex-snapshot
Coarse-Graining the Recognition of a Glycolipid by the C-Type Lectin Mincle Receptor
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c03897openalex-snapshot
Martini 3D-OZ: A Theoretical Investigation of Solvation Shell Structures and Solvation Free Energies of Martini Coarse-Grained Proteins
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c05001openalex-snapshot
Modeling Diffusive Motion of Ferredoxin and Plastocyanin on the PSI Domain of Procholorococcus marinus MIT9313
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c05242openalex-snapshot
Free Energy, Rates, and Mechanism of Transmembrane Dimerization in Lipid Bilayers from Dynamically Unbiased Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c08043openalex-snapshot
Extending the Martini 3 Coarse-Grained Force Field to Hyaluronic Acid
inferred← citeshttps://doi.org/10.1021/acs.jpcb.5c07830openalex-snapshot
Interaction of Choline-Based Ionic Liquids with Model Lipid Membranes: Force-Field Parametrization and Membrane Partitioning
inferred← citeshttps://doi.org/10.1021/acs.jpcb.6c00050openalex-snapshot
Martini 3 as a Transferable Force Field for Lipopolysaccharide Parametrization
inferred← citeshttps://doi.org/10.1021/acs.jpcb.6c02507openalex-snapshot
Assessing the Martini Force Field for Modeling Polyolefin Nanoplastics near Lipid Membranes
inferred← citeshttps://doi.org/10.1021/acs.jpcb.9b08057openalex-snapshot
Progressive Hydrophobicity of Fluorobenzenes
inferred← citeshttps://doi.org/10.1021/acs.jpcb.9b09915openalex-snapshot
Promising Route for the Development of a Computational Framework for Self-Assembly and Phase Behavior Prediction of Ionic Surfactants Using MARTINI
inferred← citeshttps://doi.org/10.1021/acs.jpclett.9b02868openalex-snapshot
An Allosteric Pathway in Copper, Zinc Superoxide Dismutase Unravels the Molecular Mechanism of the G93A Amyotrophic Lateral Sclerosis-Linked Mutation
inferred← citeshttps://doi.org/10.1021/acs.langmuir.0c01898openalex-snapshot
Microphase Arrangement of Smart Superhydrophilic Segmented Polyurethanes at Their Interface with Water
inferred← citeshttps://doi.org/10.1021/acs.langmuir.3c03474openalex-snapshot
Structure of the Bacterial Cell Envelope and Interactions with Antimicrobials: Insights from Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1021/acs.macromol.0c00877openalex-snapshot
Microscopic Understanding of the Granular Structure and the Swelling of PEDOT:PSS
inferred← citeshttps://doi.org/10.1021/acs.macromol.1c00444openalex-snapshot
Electronic, Optical, Morphological, Transport, and Electrochemical Properties of PEDOT: A Theoretical Perspective
inferred← citeshttps://doi.org/10.1021/acs.macromol.5c00273openalex-snapshot
Coarse-Grained Parameters for Simulations of Methyl-Methacrylate-Based Polymer Brushes That Reproduce Experimental Swelling Coefficients
inferred← citeshttps://doi.org/10.1021/acs.macromol.6c00951openalex-snapshot
Side-Chain Grafting Frequency Controls Trap Formation and Polaron Mobility in Organic Mixed Conductors
inferred← citeshttps://doi.org/10.1021/acs.molpharmaceut.4c00328openalex-snapshot
A Coarse-Grained Molecular Dynamics Perspective on the Release of 5-Fluorouracil from Liposomes
inferred← citeshttps://doi.org/10.1021/acs.molpharmaceut.4c00744openalex-snapshot
Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery
inferred← citeshttps://doi.org/10.1021/acs.nanolett.1c03584openalex-snapshot
Mapping Mechanostable Pulling Geometries of a Therapeutic Anticalin/CTLA-4 Protein Complex
inferred← citeshttps://doi.org/10.1021/acsami.0c08454openalex-snapshot
Evolution and Morphology of Thin Films Formed by Solvent Evaporation: An Organic Semiconductor Case Study
inferred← citeshttps://doi.org/10.1021/acsbiomaterials.3c00636openalex-snapshot
Molecular Dynamics Simulations for Rationalizing Polymer Bioconjugation Strategies: Challenges, Recent Developments, and Future Opportunities
inferred← citeshttps://doi.org/10.1021/acscentsci.5c00755openalex-snapshot
The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior
inferred← citeshttps://doi.org/10.1021/acsnano.0c07128openalex-snapshot
Properties of DNA- and Protein-Scaffolded Lipid Nanodiscs
inferred← citeshttps://doi.org/10.1021/acsomega.2c06248openalex-snapshot
Approaches and Perspective of Coarse-Grained Modeling and Simulation for Polymer–Nanoparticle Hybrid Systems
inferred← citeshttps://doi.org/10.1021/acsomega.6c02457openalex-snapshot
Amphipathic β-Sheet-Forming Octapeptide Self-Assembly Using the Martini Potential Family
inferred← citeshttps://doi.org/10.1021/jacs.6c05871openalex-snapshot
Sequence-Directed Hierarchy of Supramolecular Peptide Bilayers and Heme Cofactor Insertion
inferred← citeshttps://doi.org/10.1021/jacsau.5c00174openalex-snapshot
Simulation of Neurotrophin Receptor Transmembrane Helix Interactions Reveals Active States and Distinct Signaling Mechanisms
inferred← citeshttps://doi.org/10.1038/s41467-020-15554-9openalex-snapshot
Membrane mediated toppling mechanism of the folate energy coupling factor transporter
inferred← citeshttps://doi.org/10.1038/s41467-020-17437-5openalex-snapshot
Protein–ligand binding with the coarse-grained Martini model
inferred← citeshttps://doi.org/10.1038/s41467-021-23756-yopenalex-snapshot
Allosteric modulation of ghrelin receptor signaling by lipids
inferred← citeshttps://doi.org/10.1038/s41467-024-50647-9openalex-snapshot
Rescaling protein-protein interactions improves Martini 3 for flexible proteins in solution
inferred← citeshttps://doi.org/10.1038/s41467-025-58719-0openalex-snapshot
GōMartini 3: From large conformational changes in proteins to environmental bias corrections
inferred← citeshttps://doi.org/10.1038/s41477-022-01145-7openalex-snapshot
A conformational switch in the SCF-D3/MAX2 ubiquitin ligase facilitates strigolactone signalling
inferred← citeshttps://doi.org/10.1038/s41524-025-01729-9openalex-snapshot
Refining coarse-grained molecular topologies: a Bayesian optimization approach
inferred← citeshttps://doi.org/10.1038/s41592-021-01098-3openalex-snapshot
Martini 3: a general purpose force field for coarse-grained molecular dynamics
inferred← citeshttps://doi.org/10.1038/s41598-021-83374-yopenalex-snapshot
Effect of palmitoylation on the dimer formation of the human dopamine transporter
inferred← citeshttps://doi.org/10.1038/s41598-023-32475-xopenalex-snapshot
Effect of cetrimonium carrier micelles on bacterial membranes and extracellular DNA, an in silico study
inferred← citeshttps://doi.org/10.1038/s41598-026-50650-8openalex-snapshot
Challenges of conventional iterative all-atom and coarse-grained multiscale molecular dynamics
inferred← citeshttps://doi.org/10.1038/s42003-025-07478-1openalex-snapshot
Dynamics and activation of membrane-bound B cell receptor assembly
inferred← citeshttps://doi.org/10.1038/s42004-021-00603-1openalex-snapshot
Acyl-chain saturation regulates the order of phosphatidylinositol 4,5-bisphosphate nanodomains
inferred← citeshttps://doi.org/10.1039/d0cp01006eopenalex-snapshot
The coarse-grained models of poly(ethylene oxide) and poly(propylene oxide) homopolymers and poloxamers in big multipole water (BMW) and MARTINI frameworks
inferred← citeshttps://doi.org/10.1039/d0fd00058bopenalex-snapshot
Estimating the accuracy of the MARTINI model towards the investigation of peripheral protein–membrane interactions
inferred← citeshttps://doi.org/10.1039/d0gc01823fopenalex-snapshot
Martini coarse-grained models of imidazolium-based ionic liquids: from nanostructural organization to liquid–liquid extraction
inferred← citeshttps://doi.org/10.1039/d1cp04237hopenalex-snapshot
Martini 3 coarse-grained force field for poly( para -phenylene ethynylene)s
inferred← citeshttps://doi.org/10.1039/d1nr04610aopenalex-snapshot
Complex nanoemulsion for vitamin delivery: droplet organization and interaction with skin membranes
inferred← citeshttps://doi.org/10.1039/d2cp02655dopenalex-snapshot
Why does solvent treatment increase the conductivity of PEDOT : PSS? Insight from molecular dynamics simulations
inferred← citeshttps://doi.org/10.1039/d2cp03497bopenalex-snapshot
The impact of bilayer composition on the dimerization properties of the Slg1 stress sensor TMD from a multiscale analysis
inferred← citeshttps://doi.org/10.1039/d2cp03762aopenalex-snapshot
HRMAS-NMR and simulation study of the self-assembly of surfactants on carbon nanotubes
inferred← citeshttps://doi.org/10.1039/d2nr07069copenalex-snapshot
Bilayer lipid membrane formation on surface assemblies with sparsely distributed tethers
inferred← citeshttps://doi.org/10.1039/d2ra00732kopenalex-snapshot
A Martini 3 coarse-grain model for the simulation of the photopolymerizable organic phase in dental composites
inferred← citeshttps://doi.org/10.1039/d2ra05268gopenalex-snapshot
The concentration-dependent effect of hydrocortisone on the structure of model lung surfactant monolayer by using an in silico approach
inferred← citeshttps://doi.org/10.1039/d3cp05907copenalex-snapshot
Martinoid: the peptoid martini force field
inferred← citeshttps://doi.org/10.1039/d3em00081hopenalex-snapshot
Partitioning into phosphatidylcholine–cholesterol membranes: liposome measurements, coarse-grained simulations, and implications for bioaccumulation
inferred← citeshttps://doi.org/10.1039/d4cp04377dopenalex-snapshot
Enhanced transdermal permeation of caffeine through a skin model using electric field-induced lipid vesicles: a novel approach for drug transport
inferred← citeshttps://doi.org/10.1039/d4em00649fopenalex-snapshot
Predicting aquatic toxicity of anionic hydrocarbon and perfluorinated surfactants using membrane-water partition coefficients from coarse-grained simulations
inferred← citeshttps://doi.org/10.1039/d4nr02074jopenalex-snapshot
Nanomechanical footprint of SARS-CoV-2 variants in complex with a potent nanobody by molecular simulations
inferred← citeshttps://doi.org/10.1039/d4re00505hopenalex-snapshot
Bridging molecular dynamics and process engineering to predict the chemical recyclability of polyurethane foams
inferred← citeshttps://doi.org/10.1039/d5nr05519aopenalex-snapshot
Multiscale simulations reveal the driving forces underlying V337M-induced tau core fragment aggregation
inferred← citeshttps://doi.org/10.1039/d5sm00261copenalex-snapshot
Thermodynamic anatomy of micelle-small molecule coacervation
inferred← citeshttps://doi.org/10.1039/d5va00237kopenalex-snapshot
Coarse-grained simulations of sulfanilamide and hexachlorobenzene mobility in soil organic matter
inferred← citeshttps://doi.org/10.1039/d6cp00414hopenalex-snapshot
Aggregation behavior of sodium caprate under different pH, concentration, and intestinal fluid conditions: a coarse-grained molecular dynamics study comparing Martini 2 and Martini 3
inferred← citeshttps://doi.org/10.1039/d6cp02188copenalex-snapshot
Simulation of protein structure using a coarse-grained potential incorporating the backbone dihedral interactions
inferred← citeshttps://doi.org/10.1042/bsr20211406openalex-snapshot
Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us?
inferred← citeshttps://doi.org/10.1063/1.5119101openalex-snapshot
Resolution limit of data-driven coarse-grained models spanning chemical space
inferred← citeshttps://doi.org/10.1063/5.0046333openalex-snapshot
Spontaneous lipid binding to the nicotinic acetylcholine receptor in a native membrane
inferred← citeshttps://doi.org/10.1063/5.0058510openalex-snapshot
Modeling of thermosensitive stereoregular polymers within the coarse-grained force field: Poly(N-isopropylacrylamide) as a benchmark case
inferred← citeshttps://doi.org/10.1063/5.0095523openalex-snapshot
Small ionic radii limit time step in Martini 3 molecular dynamics simulations
inferred← citeshttps://doi.org/10.1063/5.0104914openalex-snapshot
Broad chemical transferability in structure-based coarse-graining
inferred← citeshttps://doi.org/10.1063/5.0236427openalex-snapshot
Self-assembly of architected macromolecules: Bridging a gap between experiments and simulations
inferred← citeshttps://doi.org/10.1063/5.0275282openalex-snapshot
Protein dimerization in 2D vs 3D: Geometric allostery enhances binding affinity
inferred← citeshttps://doi.org/10.1063/5.0307183openalex-snapshot
In search of shape in the unshaped: Constructing ensembles of intrinsically disordered proteins
inferred← citeshttps://doi.org/10.1063/5.0316662openalex-snapshot
Active subspace learning for coarse-grained molecular dynamics
inferred← citeshttps://doi.org/10.1063/5.0324705openalex-snapshot
Knowledge distillation of noisy force labels for improved coarse-grained force fields
inferred← citeshttps://doi.org/10.1063/9780735425279_001openalex-snapshot
A Practical Introduction to Martini 3 and its Application to Protein-Ligand Binding Simulations
inferred← citeshttps://doi.org/10.1063/9780735425279_004openalex-snapshot
A Guide to Titratable Martini Simulations
inferred← citeshttps://doi.org/10.1073/pnas.2113297119openalex-snapshot
Machine learning–driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins
inferred← citeshttps://doi.org/10.1073/pnas.2408071121openalex-snapshot
Intrinsically disordered region amplifies membrane remodeling to augment selective ER-phagy
inferred← citeshttps://doi.org/10.1080/08927022.2025.2467834openalex-snapshot
Development of a coarse-grained model for the early stages of ordered mesoporous silica formation
inferred← citeshttps://doi.org/10.1080/08927022.2025.2608034openalex-snapshot
Coarse-grained model-assisted rational design of drug delivery systems: mechanistic insights and translational perspectives
inferred← citeshttps://doi.org/10.1080/19420862.2026.2645310openalex-snapshot
Structure-based calculation of excipient effects on the viscosity of concentrated antibody solutions
inferred← citeshttps://doi.org/10.1083/jcb.202112068openalex-snapshot
Seipin concentrates distinct neutral lipids via interactions with their acyl chain carboxyl esters
inferred← citeshttps://doi.org/10.1093/glycob/cwab017openalex-snapshot
Development of Martini 2.2 parameters forN-glycans: a case study of the HIV-1 Env glycoprotein dynamics
inferred← citeshttps://doi.org/10.1093/pnasnexus/pgaf202openalex-snapshot
Microtubules in Martini: Parameterizing a heterogeneous elastic-network towards a mechanically accurate microtubule
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