ArticleJournal of chemical theory and computation2022
Extending the Martini 3 Coarse-Grained Force Field to 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 10 papers.
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Who cites it
10 citing papers in PubMed, 42 citations in OpenAlex.
- A Coarse-Grained MARTINI Model for Mucins.Journal of chemical theory and computation · 2026Article
- Computational methods in physical virology: a critical perspective across lengths and timescales.FEMS microbiology reviews · 2026Review
- Extending the Martini 3 Coarse-Grained Force Field to Hyaluronic Acid.The journal of physical chemistry. B · 2025Article
- Integrating computational insights in gold nanoparticle-mediated drug delivery: enhancing efficacy and precision.Frontiers in medical technology · 2025Review
- The Conformation of Glycosidic Linkages According to Various Force Fields: Monte Carlo Modeling of Polysaccharides Based on Extrapolation of Short-Chain Properties.Journal of chemical theory and computation · 2024Article
- Exploring Free Energies of Specific Protein Conformations Using the Martini Force Field.Journal of chemical theory and computation · 2024Article
- Application of molecular dynamics simulation in self-assembled cancer nanomedicine.Biomaterials research · 2023Review
- A brief history of visualizing membrane systems in molecular dynamics simulations.Frontiers in bioinformatics · 2023Article
- Approaches and Perspective of Coarse-Grained Modeling and Simulation for Polymer-Nanoparticle Hybrid Systems.ACS omega · 2022Review
- Martini 3 Coarse-Grained Force Field for Carbohydrates.Journal of chemical theory and computation · 2022Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Carbohydrates play an essential role in a large number of chemical and biochemical processes. High structural diversity and conformational heterogeneity make it problematic to link their measurable properties to molecular features. Molecular dynamics simulations carried out at the level of classical force fields are routinely applied to study the complex processes occurring in carbohydrate-containing systems, while the usefulness of such simulations relies on the accuracy of the underlying theoretical model. In this article, we present the coarse-grained force field dedicated to glucopyranose-based carbohydrates and compatible with the recent version of the Martini force field (v. 3.0). The parameterization was based on optimizing bonded and nonbonded parameters with a reference to the all-atom simulation results and the experimental data. Application of the newly developed coarse-grained carbohydrate model to oligosaccharides curdlan and cellulose displays spontaneous formation of aggregates of experimentally identified features. In contact with other biomolecules, the model is capable of recovering the protective effect of glucose monosaccharides on a lipid bilayer and correctly identifying the binding pockets in carbohydrate-binding proteins. The features of the newly proposed model make it an excellent candidate for further extensions, aimed at modeling more complex, functionalized, and biologically relevant carbohydrates.
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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.