LIMONADA

LIMONADA provides a curated database of lipid membrane models, lipid species annotations from LIPID MAPS, lipid topologies, force fields, and associated molecular dynamics (MD) simulation files to support accurate MD studies of biological membranes.

Key Features:

• Curated membrane models: A library of published membrane patches and membrane models with detailed lipid compositions reflecting organism, cell type, and organelle specificity.
• Lipid species annotation (LIPID MAPS): Lipid compositions are annotated using LIPID MAPS identifiers to standardize species nomenclature.
• Lipid topologies: Provided lipid topologies for use in molecular dynamics simulations.
• Force fields: Associated force field parameters required for MD simulations are included.
• MD simulation files: Corresponding simulation files for published membrane patches are provided to enable reproducible simulations.

Scientific Applications:

• Molecular dynamics of biological membranes: Preparation and execution of MD simulations that reflect realistic membrane compositions.
• Lipid diversity studies: Comparative analyses of lipid composition across organisms, cell types, and organelles.
• Membrane behavior and interactions: Investigation of membrane properties and interactions within cellular environments using MD-ready models.

Methodology:

Provides molecular dynamics (MD) simulation files with lipid species annotated using LIPID MAPS identifiers, together with lipid topologies, force fields, and published membrane patches.