Martini 3 Metabolome: 186 Common Metabolite Parameters for Coarse-Grained Simulations

A computational dataset containing parameters for 186 common metabolites found in bacteria and eukaryotes, parametrized within the Martini 3 force field. The work by Christopher Brasnett, last updated in May 2026, enables simulations of protein-ligand binding and membrane permeation. The 104.2 KB CSV file aims to support realistic simulations of cellular environments.

Use Cases

• Parameterizing coarse-grained molecular dynamics simulations based on the described Martini 3 force field parameters.
• Simulating protein-ligand binding interactions based on the described metabolite behavior in a biological setting.
• Studying membrane permeation of metabolites based on the showcased simulation examples.
• Conducting high-throughput simulations of metabolites interacting with other biomolecules based on the established metabolome framework.

Strengths

• Contains parameters for 186 specific metabolites, providing a defined scope for common biochemical components.
• Parameters are developed within the established Martini 3 force field framework, suggesting methodological consistency.
• The 104.2 KB file size indicates a focused, non-redundant parameter set.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment for specific simulation scales.
• The dataset's applicability is limited to the specific Martini 3 coarse-grained modeling framework.

Provenance

Source

figshare

Collection Method

Parametrization of metabolites within the Martini 3 force field framework, as described in the associated work.

Freshness

Last updated 2026-05-26 23:43:23; freshness should be verified.