☆ 4.6 Review

Two decades of Martini: Better beads, broader scope

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2023)

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The role of plasmalogens, Forssman lipids, and sphingolipid hydroxylation in modulating the biophysical properties of the epithelial plasma membrane

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Seipin accumulates and traps diacylglycerols and triglycerides in its ring-like structure

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Lipid regulation of hERG1 channel function

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Martini 3 Coarse-Grained Model for Type III Deep Eutectic Solvents: Thermodynamic, Structural, and Extraction Properties

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AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics

Lorenzo Casalino et al.

Summary: The study introduced a generalizable AI-driven workflow that allows for more efficient exploration of the dynamics of molecular systems, particularly focusing on the mechanisms of infectivity of the SARS-CoV-2 virus. Several novel scientific discoveries were made, including the elucidation of the spike protein's full glycan shield, the role of spike glycans in modulating virus infectivity, and the characterization of flexible interactions between the spike protein and the human ACE2 receptor. The research also demonstrated the potential of AI in accelerating conformational sampling across different systems for future applications in SARS-CoV-2 and other molecular systems.

INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS (2021)

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Article Multidisciplinary Sciences

Structure of the hexameric fungal plasma membrane proton pump in its autoinhibited state

Sabine Heit et al.

Summary: Research has revealed the structure of hexameric Pma1 in fungal plasma membrane, providing insights into its formation and autoinhibition mechanisms for potential drug development. Molecular dynamics simulations suggest lipid-mediated contacts between monomers and a protein-induced membrane deformation that may act as a proton-attracting funnel.

SCIENCE ADVANCES (2021)

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Article Chemistry, Medicinal

Asymmetric CorA Gating Mechanism as Observed by Molecular Dynamics Simulations

Mariia Nemchinova et al.

Summary: Through biophysical simulations and experimental validation, the study revealed the mechanistic details of CorA protein in the transport of divalent metal ions, showing its asymmetric movement and channel gating mechanism. The results suggest that the structure of CorA protein can be altered through a complex network of interactions to facilitate channel opening.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)

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Article Chemistry, Physical

Addressing the Excessive Aggregation of Membrane Proteins in the MARTINI Model

Ayan Majumder et al.

Summary: The widely used MARTINI model is found to over-stabilize membrane protein aggregates, leading to a reparameterization to enhance the agreement between simulation results and experimental data. The modified MARTINI model maintains a dynamic equilibrium between protein monomers and dimers.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

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Article Chemistry, Physical

Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments

Christos Lamprakis et al.

Summary: The study suggests that Martini 2.2P overestimates the free energy of association for proteins, while Martini 3 performs better in describing the association of membrane proteins. Near-native dimer complexes are identified as minima in the free energy surface, although not always as the lowest minima.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

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Article Cell Biology

Lipids and Phosphorylation Conjointly Modulate Complex Formation of β2-Adrenergic Receptor and β-arrestin2

Kristyna Pluhackova et al.

Summary: Studies have shown that GPCR receptor phosphorylation and local membrane composition cooperatively regulate the conformation and dynamics of the GPCR-arrestin complex, which in turn affects signal transduction and the binding specificity of arrestin. Therefore, a deeper understanding of the complex GPCR regulatory mechanisms is crucial for identifying novel pathways of pharmacological intervention.

FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY (2021)

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Article Chemistry, Physical

Membrane Interactions of α-Synuclein Revealed by Multiscale Molecular Dynamics Simulations, Markov State Models, and NMR

Sarah-Beth T. A. Amos et al.

Summary: The binding of alpha-Synuclein to cell membranes is a crucial first step in the molecular pathophysiology of Parkinson's disease, with the protein adopting multiple conformations. Studies using molecular dynamics simulations, nuclear magnetic resonance, and cross-linking mass spectrometry have elucidated the interactions of alpha-Synuclein with lipid bilayers, providing insights into the mechanism of PD and potential therapeutic approaches.

JOURNAL OF PHYSICAL CHEMISTRY B (2021)

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Article Biochemical Research Methods

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

Paulo C. T. Souza et al.

Summary: The refined Martini 3 model offers improved interaction balance and expanded ability to include specific interactions, allowing for more accurate predictions of molecular packing and interactions. It has been successfully applied in a wide range of applications, demonstrating its versatility and effectiveness in biomolecular simulations.

NATURE METHODS (2021)

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Editorial Material Biochemical Research Methods

Integrating experiments, theory and simulations into whole-cell models

Zaida Luthey-Schulten

NATURE METHODS (2021)

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Editorial Material Biochemical Research Methods

50 years of PBD: a catalyst in structural biology

Alexandre M. J. J. Bonvin

NATURE METHODS (2021)

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Review Polymer Science

Chemically specific coarse-graining of polymers: Methods and prospects

Satyen Dhamankar et al.

Summary: Coarse-grained modeling is crucial for studying polymers and soft matter systems, with a growing need to expand capabilities for diverse systems with chemical specificity. This review discusses essential techniques, methodologies, challenges, and recent applications of machine learning in enhancing coarse-grained modeling strategies for polymers. It provides a comprehensive discussion of methods and prospects for chemically specific coarse-graining of polymers, serving as a valuable resource for researchers in the field.

JOURNAL OF POLYMER SCIENCE (2021)

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Article Biochemistry & Molecular Biology

Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations

Paulo C. T. Souza et al.

Summary: Molecular docking is crucial for rational drug design, but current techniques have limitations in protein flexibility and solvation models, as well as the use of simplified scoring functions. Recent research has introduced a coarse-grained molecular dynamics simulation method based on the Martini force field, which can predict protein/ligand binding sites and pathways without the need for any prior information. This offers a promising approach for high-throughput drug screening based on dynamic docking pipelines.

FRONTIERS IN MOLECULAR BIOSCIENCES (2021)

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Review Cell Biology

Simulating realistic membrane shapes

Weria Pezeshkian et al.

Summary: Biological membranes exhibit diversity in their shapes and complexity in chemical compositions that are linked to many cellular functions. Simulation studies using a diverse range of computational techniques are able to capture this complexity at increasing levels of realism and connect the microscopic view on protein-lipid interactions to cellular morphologies at the level of entire organelles. Recent advances highlight the understanding of this complexity, identify current bottlenecks, and sketch possible ways ahead.

CURRENT OPINION IN CELL BIOLOGY (2021)

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Article Chemistry, Medicinal

General Protocol for Constructing Molecular Models of Nanodiscs

Lisbeth R. Kjolbye et al.

Summary: Nanodisc technology is increasingly used for studying membrane proteins. A new protocol based on geometric equations in Python allows for fast and easy customization of nanodiscs, enabling automation of molecular dynamics simulations. The protocol was validated by simulating seven different nanodiscs, showing good agreement with experimental data and simulation studies.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)

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Article Chemistry, Physical

Data-driven equation for drug-membrane permeability across drugs and membranes

Arghya Dutta et al.

Summary: The study examines the relationship between passive drug-membrane permeation and acidity, using the SISSO technique to find easily interpretable equations. Lipid-tail unsaturation is found to play a key role in permeability, contributing stepwise rather than proportionally.

JOURNAL OF CHEMICAL PHYSICS (2021)

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Article Chemistry, Physical

A Martini Coarse Grained Model of Citrate-Capped Gold Nanoparticles Interacting with Lipid Bilayers

Sebastian Salassi et al.

Summary: The study focuses on the simulation of interactions between citrate-capped gold nanoparticles (CNPs) and model phosphatidylcholine lipid membranes. The findings suggest that the citrate coating is spontaneously replaced by lipids through exchange with lipid molecules, and the size and shape of the nanoparticles determine the final structural configuration of the NP-bilayer complex.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

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Article Chemistry, Physical

Association Mechanism of Peptide-Coated Metal Nanoparticles with Model Membranes: A Coarse-Grained Study

Sebastian Franco-Ulloa et al.

Summary: Functionalized metal nanoparticles coated with a polycationic cell-penetrating peptide show high cellular uptake rates. The internalization process occurs through the formation of an intermediate state with specific stabilizing interactions. This mechanism involves interactions between the peptide-coated nanoparticles and the membrane components.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

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Article Chemistry, Physical

Quantifying Membrane Curvature Sensing of Peripheral Proteins by Simulated Buckling and Umbrella Sampling

Kai Steffen Stroh et al.

Summary: Membrane curvature plays a crucial role in the organization and trafficking of membrane associated proteins. A new method has been developed to directly quantify the relative partitioning free energy of proteins as a function of membrane curvature, providing insights into the curvature sensing mechanisms of different proteins.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

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Article Chemistry, Physical

Automated Coarse-Grained Mapping Algorithm for the Martini Force Field and Benchmarks for Membrane-Water Partitioning

Thomas D. Potter et al.

Summary: An automated system for mapping and parameterizing organic molecules for use with the coarse-grained Martini force field has been proposed, which scales to larger molecules and a broader chemical space. The core of the mapping process involves a graph-based analysis of the molecule's bonding network, with special attention to coarse-grained beads in aromatic rings. The method's performance has been tested on a diverse set of 87 neutral organic molecules, demonstrating the ability to capture key partition coefficients.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

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Article Chemistry, Physical

Relative Affinities of Protein-Cholesterol Interactions from Equilibrium Molecular Dynamics Simulations

T. Bertie Ansell et al.

Summary: Specific lipid interactions with membrane proteins are crucial for protein stability and function. A method using equilibrium coarse-grained MD simulations has been developed to determine protein-lipid binding affinities, providing a robust alternative for evaluating the relative importance of different interaction sites. This method shows good agreement with experimental and density-based equilibrium methods, making it a high-throughput approach for understanding the consequences of individual binding sites in membrane protein structures.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

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Article Chemistry, Physical

CG2AT2: an Enhanced Fragment-Based Approach for Serial Multi-scale Molecular Dynamics Simulations

Owen N. Vickery et al.

Summary: Coarse-grained molecular dynamics offers a way to simulate macromolecular complexes at a reduced level of representation, allowing for longer timescales and larger simulations. This study presents an enhanced fragment-based protocol for converting such complexes to atomistic resolution, suitable for a variety of systems including integral membrane proteins. Evaluation of the approach on 11 system configurations shows promising results in accurately describing and balancing atomic-level descriptions of macromolecular complexes.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

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Article Chemistry, Physical

Nonconverged Constraints Cause Artificial Temperature Gradients in Lipid Bilayer Simulations

Sebastian Thallmair et al.

Summary: MD simulations are crucial for studying phase separation in model membrane systems, with CG models commonly used for their computational efficiency. However, temperature differences can arise in CG MD membrane simulations due to issues with the LINCS algorithm and highly constrained moieties like cholesterol, impacting membrane properties and potentially inducing phase separation. Careful consideration of simulation parameters is required to address these discrepancies.

JOURNAL OF PHYSICAL CHEMISTRY B (2021)

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Article Chemistry, Physical

Cholesterol Hinders the Passive Uptake of Amphiphilic Nanoparticles into Fluid Lipid Membranes

Ester Canepa et al.

Summary: Cholesterol content in plasma membranes affects the passive internalization of amphiphilic gold nanoparticles within lipid bilayers, leading to a significant reduction in the amount of internalized nanoparticles.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2021)

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Article Polymer Science

Water Intake and Ion Exchange in PEDOT:Tos Films upon Cyclic Voltammetry: Experimental and Molecular Dynamics Investigation

Najmeh Delavari et al.

Summary: Through a combination of experiments and simulations, the study revealed significant morphological and mass changes in the PEDOT:Tos film during oxidation/reduction processes, confirming the replacement of tosylate by chloride ions. The relative mass change between the most oxidized and reduced states was around 10-14%, and the overall material loss during voltammetry cycles indicated that a portion of the material expelled during reduction did not return during subsequent oxidation. This research provides crucial insights into the molecular processes underlying the redox process of PEDOT:Tos film, essential for improving and evaluating the performance of bioelectronic devices.

MACROMOLECULES (2021)

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Article Biochemistry & Molecular Biology

Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage

A. Manuel Liaci et al.

Summary: Human SPC has two functional paralogs with distinct proteolytic subunits, and its structure plays a key role in the specificity for SPs based on the length of their hydrophobic segments.

MOLECULAR CELL (2021)

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Article Biochemistry & Molecular Biology

ProLint: a web-based framework for the automated data analysis and visualization of lipid-protein interactions

Besian Sejdiu et al.

Summary: ProLint is a webserver that automates the analysis of MD generated files and visualization of lipid-protein interactions, offering modular analysis methods and interactive visualization tools for detailed qualitative and quantitative exploration. Additionally, it includes a database of published MD results that can be accessed by anyone.

NUCLEIC ACIDS RESEARCH (2021)

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Article Biochemistry & Molecular Biology

Modulation of adenosine A2a receptor oligomerization by receptor activation and PIP2 interactions

Wanling Song et al.

Summary: The research characterized oligomeric configurations of the adenosine A2a receptor (A2aR) and revealed that receptor activation enhances oligomerization, leading to a more diverse oligomer populations. The study also found that the binding of PIP2 to A2aR stabilizes protein-protein interactions and that A2aR oligomerization is responsive to the local membrane lipid environment, potentially modulating the formation of specific signaling complexes.

STRUCTURE (2021)

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Article Multidisciplinary Sciences

Identification and assessment of cardiolipin interactions with E. coli inner membrane proteins

Robin A. Corey et al.

Summary: The study reveals that bacterial membrane proteins bind to specific lipids, especially cardiolipin, and shows an asymmetry in lipid binding between membrane leaflets. Through molecular dynamics simulations, over 700 independent cardiolipin binding sites were identified, defining a molecular basis for high-affinity cardiolipin binding sites on bacterial membrane proteins.

SCIENCE ADVANCES (2021)

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Review Biochemistry & Molecular Biology

From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules

Marco Giulini et al.

Summary: The increasing computer power and improved accuracy of atomistic force fields have enabled researchers to study biological systems at the molecular level in detail. However, the length and time scales of many processes of interest are still out of reach for current hardware, leading to important questions remaining unanswered. Coarse-grained models, simplified representations of molecules at a lower resolution than atomistic, are commonly used in the investigation of biological physics problems, but the optimal degree of simplification remains a crucial open issue.

FRONTIERS IN MOLECULAR BIOSCIENCES (2021)

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Review Biochemistry & Molecular Biology

A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results

A. Sengar et al.

Summary: The oxDNA model is widely used in various fields and can be accessed through two open source packages. This article presents a set of example simulations with clear documentation, introducing how to simulate the model and reviewing its fundamental properties. It also outlines how simulation results can be interpreted and provides guidance on whether using oxDNA for simulating a system is worthwhile.

FRONTIERS IN MOLECULAR BIOSCIENCES (2021)

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Article Chemistry, Physical

Estimating the accuracy of the MARTINI model towards the investigation of peripheral protein-membrane interactions

Sriraksha Srinivasan et al.

Summary: This study utilized the MARTINI CG force field to investigate the membrane binding behavior of peripheral membrane proteins and peptides, finding that despite some false positives and false negatives, the model was mostly able to accurately characterize the membrane binding behavior of peripheral proteins. This suggests that transferable chemical-specific CG force fields have potential in driving future force field development efforts.

FARADAY DISCUSSIONS (2021)

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Article Biochemistry & Molecular Biology

Development of Martini 2.2 parameters for N-glycans: a case study of the HIV-1 Env glycoprotein dynamics

Srirupa Chakraborty et al.

Summary: N-linked glycans are important in biology but limited by current experimental methods. A reductive model based on Martini 2.2 force field was developed for computational study of N-glycosylation, showing good agreement with atomistic force field and potential for studying glycosylation variants to aid drug and vaccine development.

GLYCOBIOLOGY (2021)

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Article Chemistry, Multidisciplinary

Amphiphilic nanoparticles generate curvature in lipid membranes and shape liposome-liposome interfaces

E. Lavagna et al.

Summary: Research has shown that amphiphilic Au nanoparticles with a diameter of 4 nm can induce curvature in phosphatidylcholine lipid membranes, affecting the membrane structure. By investigating the behavior of NPs on the membrane surface and within the membrane core, different curvature generation processes can be observed.

NANOSCALE (2021)

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Article Chemistry, Multidisciplinary

Coacervate formation studied by explicit solvent coarse-grain molecular dynamics with the Martini model

Maria Tsanai et al.

Summary: Complex coacervates are liquid-liquid phase separated systems containing oppositely charged polyelectrolytes, studied for their dynamic nature and functional properties. Simulation of their diffusion and partitioning is crucial for understanding their characteristics.

CHEMICAL SCIENCE (2021)

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Article Computer Science, Artificial Intelligence

Machine-learning-based dynamic-importance sampling for adaptive multiscale simulations

Harsh Bhatia et al.

Summary: The method couples different scales using dynamic-importance sampling approach, providing effective precision at macro scale with automatic feedback and self-healing capabilities. Through machine learning, it enables multiscale scientific campaigns and promises exhaustive multiscale explorations for tackling scientific problems.

NATURE MACHINE INTELLIGENCE (2021)

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Article Biochemistry & Molecular Biology

Role of cholesterol-mediated effects in GPCR heterodimers

Xavier Prasanna et al.

CHEMISTRY AND PHYSICS OF LIPIDS (2020)

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Article Chemistry, Physical

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

Hanif M. Khan et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

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Article Biochemistry & Molecular Biology

To infect or not to infect: molecular determinants of bacterial outer membrane vesicle internalization by host membranes

Damien Jefferies et al.

JOURNAL OF MOLECULAR BIOLOGY (2020)

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Article Chemistry, Multidisciplinary

Phase Separation in Atomistic Simulations of Model Membranes

Ruo-Xu Gu et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)

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Article Multidisciplinary Sciences

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

Carsten F. E. Schroer et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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Article Multidisciplinary Sciences

Multiple lipid binding sites determine the affinity of PH domains for phosphoinositide-containing membranes

Eiji Yamamoto et al.

SCIENCE ADVANCES (2020)

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Article Chemistry, Multidisciplinary

Molecular and Coarse-Grained Modeling to Characterize and Optimize Dendrimer-Based Nanocarriers for Short Interfering RNA Delivery

Filip Stojceski et al.

ACS OMEGA (2020)

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Article Biophysics

Lipid-Protein Interactions Are a Unique Property and Defining Feature of G Protein-Coupled Receptors

Besian Sejdiu et al.

BIOPHYSICAL JOURNAL (2020)

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Review Biochemistry & Molecular Biology

Multiscale modelling and simulation of viruses

Jan K. Marzinek et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2020)

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Article Chemistry, Multidisciplinary

Fats' Love-Hate Relationships: A Molecular Dynamics Simulation and Hands-On Experiment Outreach Activity to Introduce the Amphiphilic Nature and Biological Functions of Lipids to Young Students and the General Public

Anna Sofia Tascini et al.

JOURNAL OF CHEMICAL EDUCATION (2020)

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Article Chemistry, Multidisciplinary

Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism

Jacob D. Durrant et al.

ACS CENTRAL SCIENCE (2020)

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Article Multidisciplinary Sciences

Influenza hemagglutinin drives viral entry via two sequential intramembrane mechanisms

Anna Pabis et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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Article Multidisciplinary Sciences

Defining how multiple lipid species interact with inward rectifier potassium (Kir2) channels

Anna L. Duncan et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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Article Chemistry, Physical

Dual Resolution Membrane Simulations Using Virtual Sites

Yang Liu et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2020)

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Article Multidisciplinary Sciences

Membrane mediated toppling mechanism of the folate energy coupling factor transporter

Ignacio Faustino et al.

NATURE COMMUNICATIONS (2020)

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Article Multidisciplinary Sciences

Backmapping triangulated surfaces to coarse-grained membrane models

Weria Pezeshkian et al.

NATURE COMMUNICATIONS (2020)

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Article Chemistry, Multidisciplinary

Self-Sorted, Random, and Block Supramolecular Copolymers via Sequence Controlled, Multicomponent Self-Assembly

Aritra Sarkar et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)

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Article Biochemical Research Methods

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

Fude Sun et al.

PLoS Computational Biology (2020)

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Article Biology

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

Bart M. H. Bruininks et al.

ELIFE (2020)

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Article Biology

Effect of helical kink in antimicrobial peptides on membrane pore formation

Alzbeta Tuerkova et al.

ELIFE (2020)

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Article Cell Biology

Localization Preference of Antimicrobial Peptides on Liquid-Disordered Membrane Domains

Juanjuan Su et al.

FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY (2020)

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Article Materials Science, Multidisciplinary

Large scale mobility calculations in PEDOT (Poly(3,4-ethylenedioxythiophene)): Backmapping the coarse-grained MARTINI morphology

Nicolas Rolland et al.

COMPUTATIONAL MATERIALS SCIENCE (2020)

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Article Chemistry, Multidisciplinary

Self-Aggregation to Construct Hydroxide Highways in Anion Exchange Membranes

Yinfeng Yang et al.

ADVANCED MATERIALS INTERFACES (2020)

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Article Chemistry, Medicinal

Extending the Martini Coarse-Grained Force Field to N-Glycans

Aishwary T. Shivgan et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

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Article Chemistry, Physical

ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field

Xiaohua Zhang et al.

JOURNAL OF CHEMICAL PHYSICS (2020)

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Article Chemistry, Physical

Titratable Martini model for constant pH simulations

Fabian Grunewald et al.

JOURNAL OF CHEMICAL PHYSICS (2020)

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Article Chemistry, Physical

Scalable molecular dynamics on CPU and GPU architectures with NAMD

James C. Phillips et al.

JOURNAL OF CHEMICAL PHYSICS (2020)

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Article Chemistry, Physical

Coupling Coarse-Grained to Fine-Grained Models via Hamiltonian Replica Exchange

Yang Liu et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

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Article Chemistry, Physical

Developing a Coarse-Grained Model for Bacterial Cell Walls: Evaluating Mechanical Properties and Free Energy Barriers

Rakesh Vaiwala et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

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Article Chemistry, Physical

Improved coarse-grain model to unravel the phase behavior of 1-alkyl-3-methylimidazolium-based ionic liquids through molecular dynamics simulations

Emanuel A. Crespo et al.

JOURNAL OF COLLOID AND INTERFACE SCIENCE (2020)

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Article Biology

Understanding the synergistic effect of physicochemical properties of nanoparticles and their cellular entry pathways

Jiaqi Lin et al.

COMMUNICATIONS BIOLOGY (2020)

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Article Chemistry, Multidisciplinary

Resolving Donor-Acceptor Interfaces and Charge Carrier Energy Levels of Organic Semiconductors with Polar Side Chains

Riccardo Alessandri et al.

ADVANCED FUNCTIONAL MATERIALS (2020)

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Article Polymer Science

Microscopic Understanding of the Granular Structure and the Swelling of PEDOT:PSS

Mohsen Modarresi et al.

MACROMOLECULES (2020)

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Article Biophysics

Piezo1 Forms Specific, Functionally Important Interactions with Phosphoinositides and Cholesterol

Amanda Buyan et al.

BIOPHYSICAL JOURNAL (2020)

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Article Chemistry, Physical

Supramolecular-covalent hybrid polymers for light-activated mechanical actuation

Chuang Li et al.

NATURE MATERIALS (2020)

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Article Multidisciplinary Sciences

Protein-ligand binding with the coarse-grained Martini model

Paulo C. T. Souza et al.

NATURE COMMUNICATIONS (2020)

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Article Multidisciplinary Sciences

Triacylglycerols sequester monotopic membrane proteins to lipid droplets

Lucie Caillon et al.

NATURE COMMUNICATIONS (2020)

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Article Chemistry, Physical

Computer simulations of a heterogeneous membrane with enhanced sampling techniques

Yevhen K. Cherniavskyi et al.

JOURNAL OF CHEMICAL PHYSICS (2020)

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Article Polymer Science

Chain Conformation and Hydration of Polyethylene Oxide Grafted to Gold Nanoparticles: Curvature and Chain Length Effect

Udaya Dahal et al.

MACROMOLECULES (2020)

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Article Multidisciplinary Sciences

Exploring the landscape of model representations

Thomas T. Foley et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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Article Multidisciplinary Sciences

Reconstitution of autophagosome nucleation defines Atg9 vesicles as seeds for membrane formation

Justyna Sawa-Makarska et al.

SCIENCE (2020)

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Article Chemistry, Physical

Coarse graining molecular dynamics with graph neural networks

Brooke E. Husic et al.

JOURNAL OF CHEMICAL PHYSICS (2020)

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Article Biochemistry & Molecular Biology

CGMD Platform: Integrated Web Servers for the Preparation, Running, and Analysis of Coarse-Grained Molecular Dynamics Simulations

Alessandro Marchetto et al.

MOLECULES (2020)

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Article Multidisciplinary Sciences

Integrative modeling of membrane-associated protein assemblies

Jorge Roel-Touris et al.

NATURE COMMUNICATIONS (2020)

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Article Chemistry, Multidisciplinary

Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-Based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization

Charly Empereur-Mot et al.

ACS OMEGA (2020)

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Article Multidisciplinary Sciences

Dispersion state phase diagram of citrate-coated metallic nanoparticles in saline solutions

Sebastian Franco-Ulloa et al.

NATURE COMMUNICATIONS (2020)

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Article Chemistry, Multidisciplinary

Martini coarse-grained models of imidazolium-based ionic liquids: from nanostructural organization to liquid-liquid extraction

Luis Itza Vazquez-Salazar et al.

GREEN CHEMISTRY (2020)

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Article Chemistry, Multidisciplinary

Amphiphilic gold nanoparticles perturb phase separation in multidomain lipid membranes

Ester Canepa et al.

NANOSCALE (2020)

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Article Chemistry, Multidisciplinary

Size-dependent aggregation of hydrophobic nanoparticles in lipid membranes

Enrico Lavagna et al.

NANOSCALE (2020)

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Article Chemistry, Multidisciplinary

New biobased-zwitterionic ionic liquids: efficiency and biocompatibility for the development of sustainable biorefinery processes

Gael Huet et al.

GREEN CHEMISTRY (2020)

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Article Chemistry, Multidisciplinary

Decoupling copolymer, lipid and carbon nanotube interactions in hybrid, biomimetic vesicles

Joshua A. Hammons et al.

NANOSCALE (2020)

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Article Chemistry, Multidisciplinary

The aggregation of striped nanoparticles in mixed phospholipid bilayers

Sang Young Noh et al.

NANOSCALE (2020)

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Article Polymer Science

Nafion Ionomer Dispersion in Mixtures of 1-Propanol and Water Based on the Martini Coarse-Grained Model

Takuya Mabuchi et al.

JOURNAL OF POLYMER SCIENCE (2020)

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Article Biochemistry & Molecular Biology

The lipid environment of Escherichia coli Aquaporin Z

Victoria Schmidt et al.

BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES (2019)

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Article Biophysics

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

Sebastian Thallmair et al.

BIOPHYSICAL JOURNAL (2019)

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Review Chemistry, Multidisciplinary

Emerging Diversity in Lipid-Protein Interactions

Valentina Corradi et al.

CHEMICAL REVIEWS (2019)

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Review Chemistry, Multidisciplinary

Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance

Giray Enkavi et al.

CHEMICAL REVIEWS (2019)

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Article Chemistry, Physical

The SIRAH 2.0 Force Field: Altius, Fortius, Citius

Matias R. Machado et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)

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Article Chemistry, Physical

Role of Ligand Conformation on Nanoparticle-Protein Interactions

Federica Simonelli et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2019)

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Article Chemistry, Multidisciplinary

Styrene/Maleic Acid Copolymers Form SMALPs by Pulling Lipid Patches out of the Lipid Bilayer

Philipp S. Orekhov et al.

LANGMUIR (2019)

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Article Multidisciplinary Sciences

Thermodynamically reversible paths of the first fusion intermediate reveal an important role for membrane anchors of fusion proteins

Yuliya G. Smirnova et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

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Article Chemistry, Multidisciplinary

Martini bead form factors for nucleic acids and their application in the refinement of protein-nucleic acid complexes against SAXS data

Cristina Paissoni et al.

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2019)

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

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MARTINI Coarse-Grained Model for Crystalline Cellulose Microfibers

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Overview of the Effect of Salts on Biphasic Ionic Liquid/Water Solvent Extraction Systems: Anion Exchange, Mutual Solubility, and Thermomorphic Properties

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Thermodynamic and kinetic characterization of transmembrane helix association

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Nothing to Sneeze At: A Dynamic and Integrative Computational Model of an Influenza A Virion

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Coarse-Graining Poly(ethylene oxide)-Poly(propylene oxide)-Poly(ethylene oxide) (PEO-PPO-PEO) Block Copolymers Using the MARTINI Force Field

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PHYSICAL REVIEW LETTERS (2014)

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Force-Field Parameters from the SAFT-gamma Equation of State for Use in Coarse-Grained Molecular Simulations

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Improved Parameters for the Martini Coarse-Grained Protein Force Field

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Toward Optimized Potential Functions for Protein-Protein Interactions in Aqueous Solutions: Osmotic Second Virial Coefficient Calculations Using the MARTINI Coarse-Grained Force Field

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Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations

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Martini Force Field Parameters for Glycolipids

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Further Optimization of a Hybrid United-Atom and Coarse-Grained Force Field for Folding Simulations: Improved Backbone Hydration and Interactions between Charged Side Chains

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On Atomistic and Coarse-Grained Models for C60 Fullerene

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

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

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Coarse-grained molecular dynamics studies of the concentration and size dependence of fifth- and seventh-generation PAMAM dendrimers on pore formation in DMPC bilayer

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The molecular mechanism of monolayer-bilayer transformations of lung surfactant from molecular dynamics simulations

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

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The MARTINI force field: Coarse grained model for biomolecular simulations

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Polymorphic phase behavior of cardiolipin derivatives studied by coarse-grained molecular dynamics

Martin Dahlberg

JOURNAL OF PHYSICAL CHEMISTRY B (2007)

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Molecular dynamics simulations of PAMAM dendrimer-induced pore formation in DPPC bilayers with a coarse-grained model

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JOURNAL OF PHYSICAL CHEMISTRY B (2006)

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Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

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Multigraining: An algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems

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Coarse grained protein-lipid model with application to lipoprotein particles

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Insertion and assembly of membrane proteins via simulation

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JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)

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Spontaneous assembly of subnanometre-ordered domains in the ligand shell of monolayer-protected nanoparticles

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NATURE MATERIALS (2004)

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Coarse grained model for semiquantitative lipid simulations

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Development and testing of a general amber force field

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

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Equilibrium structure and lateral stress distribution of amphiphilic bilayers from dissipative particle dynamics simulations

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A coarse grain model for phospholipid simulations

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JOURNAL OF PHYSICAL CHEMISTRY B (2001)

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