Defining active residue

HADDOCK
1

Hi
I am trying to do protein-peptide docking using easy interface. I have experimental data to define active residues for the peptide but not for the active residues in protein for my peptide. However, there are few evidences defining active residues for one of the protein subtype I am docking while there is none evidence for the another subtype. But from the previous evidences, a stretch of 10-15 amino acids is identified to form an interacting site for the peptide. In this case:

  1. should I define the whole stretch of 10-15 amino acids as active residues?
  2. should I define the whole stretch of 10-15 amino acids as passive residues?
  3. should I define the certain amino acids amino acids based on evidences from other protein subtype as active residues?
  4. Or, any other advice?

Thank you
Yashad

2

Hi Yashad,

We have a protein-peptide tutorial - good to have a look to see the recommended settings. Check

https://www.bonvinlab.org/education/molmod/docking/

Also check out best practice guide:

https://www.bonvinlab.org/software/bpg/peptides/

And as for your question, you will need to define active residues at least for one of the two components.

I would start with option 1), possibly complemented by 3).

If you go for 2), be generous in the region you define as passive on the protein side.
But you will need some active residues on the peptide side.

3

Thank you Alexandre for your prompt response and recommended resources.