Small error in the Tutorial for local HADDOCK2.4

HADDOCK
1

I am doing the “Tutorial describing the use of a local version of HADDOCK2.4” and I think there’s a small error in the description of how to filter residues on their solvent accessibility. The text says that the HADDOCK server uses a 15% solvent accessibility as a cutoff (see below), but when you use FreeSASA and awk to filter residues, there seems to be a 40% cutoff. This 40% cutoff agrees with the explanation in the support manual.

This is the text that says that the HADDOCK webserver uses a 15% cutoff:

An important aspect is to filter both the active (the residues identified from your mapping experiment) and passive residues by their solvent accessibility. Our webserver uses a default relative accessibility of 15% as cutoff. This is not a hard limit. You might consider including even more buried residues if some important chemical group seems solvent accessible from a visual inspection.

This is what the text in the tutorial says, and I think the 15% is wrong here:

The following command will return all residues with a relative SASA for either the backbone or the side-chain > 15%:

awk '{if (NF==13 && $5>40) print $0; if (NF==14 && $6>40) print $0}' e2a_1F3G.rsa

Do I understand it correctly that 40% should be used?

2

The server does filter the user input at 15% and defines automatically passive residues around those at the same cutoff.

There is no right or wrong value. We have indeed used 40% in the past when doing manual setup / definition of active residues.

The more restraints you define at the end the longer will the computations become.

3

Thank you for your answer! I will try some cutoffs and see how long it takes.

The awk line does filter for >40% and not 15% though, right?

4

The awk line does filter for >40% and not 15% though, right?

Yes

Also, always look at what you are selecting when working on your own system. Always good to visualise things first.