Interactions

The interaction page in ChemoPar-db provides a detailed view of the molecular interactions between a specific chemokine chain and any binding partner(s) in the structure.

Interaction info page

Each interaction page includes several key sections to assist in the exploration and analysis of chemokine-partner interactions:

1. 3D view:

   • Displays a 3D representation of the chemokine-partner complex, highlighting interacting residues.

   • Users can interact with the structure by rotating, zooming, and focusing on specific contact points, enabling a detailed examination of the binding interface.

2. Chemokine diagram:

   • Displays a 2D representation of the chemokine sequence with the option to highlight interacting residues per partner.

3. Residue interaction table:

   • Lists all residues in the chemokine that interact with the binding partner, along with the specific type of interaction for each residue.

   • This table can be downloaded in Excel format.

4. Interaction fingerprint (IFP) similarity search:

   • Each chemokine-partner pair is annotated with a IFP bitstring, summarizing the contact pattern between the chemokine and partner as a bitstring.

   • This bitstring representation allows easy comparison of interaction profiles across different chemokine-partner complexes in ChemoPar-db.

   • Allows users to perform a similarity search based on the IFP, comparing the current complex to other complexes in ChemoPar-db.

   • Displays similarity scores using the Tanimoto coefficient, making it easy to identify other complexes with similar interaction patterns.

5. Ligand interaction network (if applicable):

   • If the complex involves a small molecule or other ligand, an interaction network visualization is generated.

   • This network illustrates the specific contacts between the chemokine, its binding partner, and the ligand.