AH-DB

AH-DB provides a curated collection of 746,314 apo-holo protein structure pairs from the Protein Data Bank (PDB) to support analysis of protein conformational transitions between unbound (apo) and bound (holo) states.

Key Features:

• Extensive Data Collection: Contains 746,314 apo-holo pairs identified and mapped from Protein Data Bank (PDB) entries.
• Refined Alignment Scheme: Applies a refined alignment scheme to accurately identify conformational transitions and pair apo and holo structures.
• Fragment Handling: Accounts for incomplete protein fragments in PDB entries to enable pairing of partial structures.

Scientific Applications:

• Enzyme Activity Regulation: Supports analysis of conformational changes that regulate enzyme activity.
• Ligand Binding: Enables investigation of structural transitions associated with ligand binding.
• Signal Transduction: Facilitates study of conformational changes involved in signal transduction pathways.
• SOD1 Conformational Study: Can be used to investigate copper-zinc superoxide dismutase (SOD1) transitions between 'open' apo and 'closed' holo states.

Methodology:

Molecules are identified and mapped from PDB entries, and a refined alignment scheme is applied to pair apo and holo structures while accommodating incomplete protein fragments.