MemProtMD

MemProtMD automates the assembly of membrane protein structures from the Protein Data Bank (PDB) into simulated lipid bilayers using Coarse-Grained Self Assembly Molecular Dynamics simulations and provides lipid contact and topology data to support studies of membrane protein structure and function.

Key Features:

• Automated Lipid Bilayer Assembly: The pipeline assembles PDB membrane protein structures into lipid bilayers using Coarse-Grained Self Assembly Molecular Dynamics simulations.
• Database Content: The resource reports a database that includes over 5000 assembled structures and references ensemble analyses performed across 3506 PDB entries.
• Lipid Contact and Topology Data: Provides per-residue lipid contact data and membrane protein topology annotations linked to PDB and UniProt identifiers and annotated with Pfam, Gene Ontology, mpstruc, and the Transporter Classification Database.
• Ensemble Analyses: Performs ensemble analyses to identify conserved lipid interaction patterns across proteins, families, and database-wide entries.
• Simulation Files: Supplies files required to run further molecular simulations on the assembled membrane protein systems.

Scientific Applications:

• Membrane protein–lipid interaction analysis: Enables characterization of protein–lipid contact patterns and identification of lipid-binding sites from PDB-derived structures.
• Functional interpretation: Supports studies of membrane protein roles in cell signaling, molecular transport, and bioenergetics.
• Comparative and family-level studies: Facilitates comparative analyses across protein families using Pfam, Gene Ontology, mpstruc, and Transporter Classification Database annotations.

Methodology:

Automated integration of newly released PDB membrane protein structures into lipid bilayers using Coarse-Grained Self Assembly Molecular Dynamics simulations and subsequent ensemble analyses to identify conserved lipid interaction patterns.