IDPsBind

IDPsBind catalogs binding sites between intrinsically disordered proteins (IDPs) and their interacting ligands derived from known 3D structures in the Protein Data Bank (PDB) to support analysis of IDP–ligand interactions.

Key Features:

• Binding site repository: Catalogs interaction sites between intrinsically disordered proteins (IDPs) and their interacting ligands extracted from known 3D structures in the Protein Data Bank (PDB).
• Identification method: Employs a distance threshold method to identify interacting residues and binding sites from PDB structures.
• Dataset scope: Contains 9,626 IDP complexes involving 880 intrinsically disordered proteins (version 1.0).
• Experimental validation: Entries are derived from experimentally determined structures and thus reflect experimentally verified interaction sites.

Scientific Applications:

• Interaction mechanism analysis: Enables analysis of IDP–ligand interaction mechanisms using experimentally derived binding-site data.
• Algorithm development: Provides a benchmark dataset for development and evaluation of algorithms that predict interaction sites in IDPs.
• Computational biology research: Supports studies of protein interactions and the functional roles of intrinsically disordered proteins in cellular processes.

Methodology:

Interaction sites were identified from experimentally determined 3D structures in the PDB using a distance threshold method.