iLipidDyn

iLipidDyn analyzes molecular dynamics (MD) simulations of cellular membranes to quantify lipidomic composition and membrane properties relevant to protein–membrane interactions.

Key Features:

• Integration with lipidomic data: Leverages high-throughput lipidomic data to estimate membrane composition at subcellular levels and to design biologically relevant models for MD simulations.
• Comprehensive membrane property analyses: Computes area per lipid, thickness, order parameters, diffusion motions, lipid density, and lipid enrichment/depletion.
• Average and time-series analyses: Provides both average properties and time series analyses for selected membrane characteristics.
• Efficient data handling and parallelization: Optimized to process large MD simulation datasets and employs parallelization techniques for data processing.
• Python implementation: Implemented in Python for computational analyses.
• Graphical publication-ready outputs: Generates graphical outputs intended for publication.

Scientific Applications:

• Subcellular membrane composition analysis: Simulates and analyzes membrane compositions that vary across cellular compartments.
• Protein–membrane interaction studies: Investigates interactions between membranes and proteins, including analyses of transmembrane protein domains.
• Disease-associated lipid studies: Examines changes in membrane lipids that are associated with various diseases.

Methodology:

Collects MD simulation data; leverages high-throughput lipidomic data to estimate membrane composition and design simulation models; computes average properties and time-series analyses for selected membrane characteristics; employs parallelization for large-scale data processing; implemented in Python.