AHoJ: Apo Holo Protein Search

AHoJ: Apo Holo Protein Search retrieves and aligns apoprotein (unbound) and corresponding holo (ligand-bound) structures from the Protein Data Bank (PDB) to identify and analyze ligand-bound versus unbound conformational states.

Key Features:

• Customizable search: Searches the Protein Data Bank (PDB) for apoprotein–holo structure pairs based on user-defined query structures and ligands.
• Alignment capabilities: Aligns retrieved structures to a query and superimposes binding sites to assess conformational differences.
• Apo/holo classification: Classifies each structure as apo or holo relative to the query by examining occupancy of the superimposed binding site.
• Batch processing: Supports batch operations and parallel processing for large-scale retrieval and alignment tasks.
• Visualization integration: Integrates with visualization software such as Mol* (Molstar) and PyMOL for inspection of aligned structures.
• Public API access: Provides a REST API for programmatic integration into bioinformatics workflows.

Scientific Applications:

• Mechanism elucidation: Enables comparison of apo and holo states to study conformational dynamics involved in protein function.
• Ligand design: Facilitates identification of structural changes upon ligand binding to inform ligand optimization and design.
• Structural analysis: Supports comparative studies of protein structures across states to evaluate conserved features and the effects of modifications.

Methodology:

Accepts user-defined query structures and ligands, retrieves relevant PDB entries that feature the same binding sites as the query, aligns these structures, and examines superimposed binding sites to classify each structure as apo or holo relative to the query.