HADDOCK3 Docking Results Analysis

HADDOCK
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Dear experts,

May I ask if there is anyone here who has experience using haddock3 or other tools for antigen-antibody docking or protein-protein docking? I would like to seek your advice on the following:

  1. During docking, I constrained the residues in the red-highlighted region as the active residues of the antigen. In the best docking result, interactions between the red region residues and the CDR regions were indeed observed. However, other amino acid residues in the surrounding structure (outside the red region) also show significant hydrogen bond interactions with the antibody. Is this considered normal?

  2. As shown at the bottom of the figure, some residues outside the antibody’s CDR regions appear to interact with other structural domains of the antigen. Is this phenomenon reasonable?

(Figure: The image shows the best docking result obtained from constrained docking using haddock3. Green represents the antigen. The red-highlighted segment of the antigen was experimentally synthesized and confirmed to be the primary region interacting with the antibody. Dark blue and cyan represent the Fv region of the antibody, while yellow and orange are used to mark the antibody’s CDR regions.)

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  1. During docking, I constrained the residues in the red-highlighted region as the active residues of the antigen. In the best docking result, interactions between the red region residues and the CDR regions were indeed observed. However, other amino acid residues in the surrounding structure (outside the red region) also show significant hydrogen bond interactions with the antibody. Is this considered normal?

Yes of course. Other parts can indeed interact.

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Thank you so much for your prompt and clear reply! It really helps me confirm my docking results and dispel my doubts.