ArticleJournal of chemical theory and computation2022
Martini 3 Coarse-Grained Force Field for Carbohydrates.
Article in Journal of chemical theory and computation, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
40 citing papers in PubMed.
- Martini 3 Coarse-Grained Model of DNA for Heterogeneous Molecular Systems.bioRxiv : the preprint server for biology · 2026Article
- Computational modeling of lignin: from molecular structure to functional properties.RSC advances · 2026Review
- Fast-Forward: Automatic Assignment and Assessment of Bonded Parameters for the Martini Force Field.Journal of chemical information and modeling · 2026Article
- Analytical coarse grained potential parameterization by reinforcement learning for anisotropic cellulose.Journal of molecular modeling · 2026Article
- Molecular Modeling of Surfactant Interaction on Phospholipid Bilayers Mimicking Corneal Epithelium.Journal of chemical theory and computation · 2026Article
- MartiniSurf: Automated Simulations of Surface-Immobilized Biomolecular Systems with Martini.Journal of chemical information and modeling · 2026Article
- Martini 3 Metabolome.Journal of chemical theory and computation · 2026Article
- Coarse-Grained Simulations of Mycobacterial Outer Membranes Reveal Fluidity-Dependent PDIM Redistribution across Different Lipid Environments.Biomacromolecules · 2026Article
- Enhanced Condensation of RNA Repeats Induced by Terahertz Oscillatory Fields.Molecules (Basel, Switzerland) · 2026Article
- Encapsulation of colistin using hyaluronic acid and PVA-PSS polymeric nanocarriers for enhanced drug delivery: a molecular dynamics simulation study.Scientific reports · 2026Article
- Martini Mapper: An Automated Fragment-Based Mapping Algorithm for Developing Coarse-Grained Models within the Martini 3 Framework.Journal of chemical information and modeling · 2026Article
- Martini 3 as a Transferable Force Field for Lipopolysaccharide Parametrization.The journal of physical chemistry. B · 2026Article
- Coarse-Grained Martini 3 Model of Chondroitin Sulfate A.Journal of chemical theory and computation · 2026Article
- Coarse-Grained Simulations of Mycobacterial Outer Membranes Reveal Fluidity-Dependent PDIM Redistribution Across Different Lipid Environments.bioRxiv : the preprint server for biology · 2026Article
- Mechanistic Determinants of Oriented Enzyme Immobilization from Martini Simulations.The journal of physical chemistry letters · 2026Article
- Coarse-grained Martini 3 model for collagen fibrils.Biophysical journal · 2026Article
- A Coarse-Grained MARTINI Model for Mucins.Journal of chemical theory and computation · 2026Article
- Bridging Scales: Coarse-Grained Protein Models in Computational Biology.Advances in experimental medicine and biology · 2026Review
- Molecular dynamics simulation in traditional Chinese medicine research: from molecular mechanisms to multiscale validation.Frontiers in chemistry · 2026Review
- Multiscale Simulation of Phosphofructokinase-1 Assemblies: Capturing the Interplay between Specific and Transient Interactions.The journal of physical chemistry. B · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Martini 3 force field is a full reparametrization of the Martini coarse-grained model for biomolecular simulations. Due to the improved interaction balance, it allows for a more accurate description of condensed phase systems. In the present work, we develop a consistent strategy to parametrize carbohydrate molecules accurately within the framework of Martini 3. In particular, we develop a canonical mapping scheme which decomposes arbitrarily large carbohydrates into a limited number of fragments. Bead types for these fragments have been assigned by matching physicochemical properties of mono- and disaccharides. In addition, guidelines for assigning bonds, angles, and dihedrals were developed. These guidelines enable a more accurate description of carbohydrate conformations than in the Martini 2 force field. We show that models obtained with this approach are able to accurately reproduce osmotic pressures of carbohydrate water solutions. Furthermore, we provide evidence that the model differentiates correctly the solubility of the polyglucoses dextran (water-soluble) and cellulose (water insoluble but soluble in ionic liquids). Finally, we demonstrate that the new building blocks can be applied to glycolipids. We show they are able to reproduce membrane properties and induce binding of peripheral membrane proteins. These test cases demonstrate the validity and transferability of our approach.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.