Some question about tutorial and with different case

HADDOCK
1

Dear Bonvinlab,

I am trying to understand the tutorial of “HADDOCK2.4 Antibody - Antigen tutorial using PDB-tools webserver” and I found my self was confuse on something I don’t understand. This below show something that I should ask you to get the answer for my better understanding.

  1. I don’t understand how to get the Active residues (directly involved in the interaction) → 26,27,28,29,30,31,32,55,56,57,101,102,103,106,108,146,147,148,150,151,152,170,172,212,213,214,215 even after using ProABC-2. After using Parapred, I found any similar to the number of active residues (in tutorial) but not all of them is used. The prediction paratope result from Parapred is:

    1. Heavy Chain
    *CDR1: 24-34
    *CDR2: 50-58
    *CDR3: 93-104
2. Light Chain
    *CDR1: 22-36
    *CDR2: 48-58
    *CDR3: 87-99

However, I found use of Chothia’s numbering scheme below.

    1. Heavy Chain
       *CDR1: 26-32
       *CDR2: 52-56
       *CDR3: 95-102
    2. Light Chain
       *CDR1: 24-34
       *CDR2: 50-56
       *CDR3: 89-97

So what should I do?

  1. In Visualisation Part, the instruction command me to superimpose all models on chain A (receptor) of the first reference structure and calculate RMSD of chain B (ligand) for which 4G6M-matched.pdb is used as the reference structure. My question is if the results of the antibody-antigen docking I’m going to do don’t have any complex from the RCSB PDB, how do I know which reference structure to use?

Thank you for replying.

Best Regards,
Syafri Izzat Abidiy

#haddock The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab

2

There are different methods of predicting the paratope. It does not matter much which one you choose, but what is important is to make sure the numbering of the predicted residues matches the numbering of the sequence in your PDB file.

As for the RMSD question, obviously in a real case you won’t know the answer and will have to trust (or not) the cluster scoring.