ArticleJournal of chemical information and modeling2025
Systematic Approach to Parametrization of Disaccharides for the Martini 3 Coarse-Grained Force Field.
Article in Journal of chemical information and modeling, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 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
8 citing papers in PubMed.
- 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
- 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
- A Coarse-Grained MARTINI Model for Mucins.Journal of chemical theory and computation · 2026Article
- Atomistic modeling of lysophospholipids from the Campylobacter jejuni lipidome.Biophysical journal · 2025Article
- The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior.ACS central science · 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
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sugars are ubiquitous in biology; they occur in all kingdoms of life. Despite their prevalence, they have often been somewhat neglected in studies of structure-dynamics-function relationships of macromolecules to which they are attached, with the exception of nucleic acids. This is largely due to the inherent difficulties of not only studying the conformational dynamics of sugars using experimental methods but indeed also resolving their static structures. Molecular dynamics (MD) simulations offer a route to the prediction of conformational ensembles and the time-dependent behavior of sugars and glycosylated macromolecules. However, at the all-atom level of detail, MD simulations are often too computationally demanding to allow a systematic investigation of molecular interactions in systems of interest. To overcome this, large scale simulations of complex biological systems have profited from advances in coarse-grained (CG) simulations. Perhaps the most widely used CG force field for biomolecular simulations is Martini. Here, we present a parameter set for glucose- and mannose-based disaccharides for Martini 3. The generation of the CG parameters from atomistic trajectories is automated as fully as possible, and where not possible, we provide details of the protocol used for manual intervention.
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.