Active Passive Residues Understanding Problem

HADDOCK
1

Hi
So I have two proteins, let’s call them X and Y. And I want to dock them.

I know the potential binding sites for X, however, I have little to zero idea about protein Y ( a smaller one)

What will be the best approach will be here?

  1. Select potential binding sites as active and go with passive from active.py for protein X, or select the potential binding sites as only passive since it isn’t nmr Data, rather bioinformatics outer membrane prediction.

  2. For protein Y, do I select the whole protein as passive?
    Or is there any way to select none of it as passive or active? I saw in one post that there was mention of selecting one residue as passive.

  3. I’m still confused about unambiguous and ambiguous thing. In my scenario it’ll be best to generate ambiguous restrain file, right?

I’ll be grateful if the questions are answered. Thank you!

2

So I have two proteins, let’s call them X and Y. And I want to dock them.
I know the potential binding sites for X, however, I have little to zero idea about protein Y ( a smaller one)
What will be the best approach will be here?
• Select potential binding sites as active and go with passive from active.py for protein X, or select the potential binding sites as only passive since it isn’t nmr Data, rather bioinformatics outer membrane prediction.

If you only have active for protein X, it does not make sense to define passive for protein X.

For protein Y you could select all solvent accessible residues as passive (an option on the server - might require expert level)

• I’m still confused about unambiguous and ambiguous thing. In my scenario it’ll be best to generate ambiguous restrain file, right

If you trust fully your active residues for protein X, you can still use those as ambiguous restraints, but turn off the random removal of restraints

3

Thank you!!

Also, it’s possible to define only passive and not active, right?

4

Also, it’s possible to define only passive and not active, right?

Yes, given that for the other protein you have defined active residues