Active Residues (Protein-protein Docking)

HADDOCK
1

Hello, I am an undergraduate student, what software can I use to identify my active residues?

Initially, I used PyMOL by inserting two proteins into the viewer, I listed residues that have close proximity to each other and defined them as my active residues, I got a HADDOCK score of -103.0 and a Z-score of -1.2. Is this way of defining active residues accepted? If not, what software should I use? Thank you in advance!

2

Hi there,

putting two proteins close to each other in PyMOL is not going to help in identifying the active residues. These amino acids are typically extracted from experimental data, but can also be identified by means of different software, depending on the situation. Among the others:

  • ProABC-2 if one of the proteins is an antibody
  • ARCTIC-3D if there is some interface information about the protein of interest in the PDB
  • CPORT or WHISCY to predict possibly interacting residues

Please have a look at the tutorials Education & Tutorials of the Bonvin Lab – Bonvin Lab on our website for a more complete picture

3

Hello, I am starting to explore now WHISCY, since CPORT is not available anymore.

I am having a problem finding the HSSP ID which is one of the requirements of WHISCY, I already tried to use instead a format from NCBI it’s stating an error. Can you please help? I am really having a hard time identifying my active residues. Thank you in advance!

4

Hi @Aron_1226, could you please share what is your error message?