TMPad

TMPad provides a curated database of experimentally observed transmembrane helix-helix interactions and pre-calculated geometric descriptors to support analysis of membrane protein helix packing, folding, and function.

Key Features:

• Integration of Experimental Data: TMPad compiles experimentally observed helix-helix interactions and related structural information from membrane proteins.
• Pre-calculated Geometric Descriptors: Pre-calculated geometric descriptors include residue backbone and side-chain contacts, interhelical distances and crossing angles, helical translational shifts, and rotational angles.
• Comprehensive Annotations: Annotations include sequence data, topology information, lipid accessibility, and ligand-binding details.
• Structural Classification and Schematic Diagrams: The database provides structural classifications and schematic diagrams representing helix-packing features.

Scientific Applications:

• Helix-packing analysis: Enables analysis of helix-helix interactions and helix-packing modes in transmembrane proteins.
• Structure–function relationships: Supports exploration of the relationship between helix-helix interactions and higher-order organization in TM protein structure and function.
• Membrane protein folding and stability: Facilitates studies of membrane protein folding, stability, and functional dynamics.
• Lipid and ligand interaction studies: Supports investigation of lipid accessibility and ligand-binding in transmembrane regions.

Methodology:

Compilation of experimentally observed helix-helix interactions and pre-calculation of geometric descriptors (residue backbone/side-chain contacts, interhelical distances, crossing angles, translational shifts, rotational angles), together with structural classification and annotation of sequence, topology, lipid accessibility, and ligand-binding details.