ArticleJournal of chemical theory and computation2026
Martini 3 Metabolome.
Article in Journal of chemical theory and computation, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
What it found
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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
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Who cites it
2 citing papers in PubMed.
- Fast-Forward: Automatic Assignment and Assessment of Bonded Parameters for the Martini Force Field.Journal of chemical information and modeling · 2026Article
- Martini 3 Metabolome.Journal of chemical theory and computation · 2026Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metabolites are ubiquitous in all living cells and are essential mediators of biochemical processes, serving either as substrates or as cofactors to enable reactions. Capturing this diversity in computational workflows is important for allowing realistic simulations of cytoplasm. Coarse-grained molecular dynamics enables the simulation of large-scale systems up to the level of whole cells but is limited by the availability of refined parameters for all possible components in the system. In this work, we describe the parametrization of 186 common metabolites found in bacteria and eukaryotes within the framework of the Martini 3 force field. To showcase the behavior of Martini metabolites in a biological setting, we report simulations of protein-ligand binding and membrane permeation. The establishment of a Martini metabolome enables high-throughput simulations of metabolites interacting with other biomolecules and opens the way for simulations of realistic cellular environments.
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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 Socratic graph.