Check best practices for the protein-peptide docking

[AnnaKravchenko]

Check which automatic changes haddock2.4 server does for protein-peptide docking and, if needed, update haddock3 protein-peptide tutorial.

[amjjbonvin]

Settings should be the same as what is defined in the protein-peptide example in haddock3 - check docking-protein-peptide-full.cfg

Mainly:

1. peptide defined as fully flexible
2. number of MD steps increased by a factor 4
3. dihedral restraints for secondary structure elements

[AnnaKravchenko]

Thanks a lot, makes it heaps easier for me!

[rvhonorato]

{
  "clust_cutoff": 5.0,
  "clust_meth": "RMSD",
  "initiosteps": 2000,
  "cool1_steps": 2000,
  "cool2_steps": 4000,
  "cool3_steps": 4000,
  "ssdihed": "alphabeta"
}

• https://github.com/haddocking/csbportal/blob/main/web/app/haddock24/tools/cns_template/protein-peptide.json

*and the criteria to decide if an amino acid chain is a peptide is >15aa

[rvhonorato]

Not sure if this is relevant for this case but also note that there is hierarchy for systems with multiple molecule types (https://github.com/haddocking/csbportal/blob/main/web/app/haddock24/views.py#L1240-L1348)

Bioinformatic predictions > Coarse-grain > Protein-Nucleic > Nucleic > Ligand > Glycan > Peptide

Meaning if your system has, for example, protein-nucleic and a peptide, the protein-nucleic has higher priority than the peptide optimal parameters - and only one of these is applied.

[AnnaKravchenko]

Not sure if this is relevant for this case but also note that there is hierarchy for systems with multiple molecule types (https://github.com/haddocking/csbportal/blob/main/web/app/haddock24/views.py#L1240-L1348)

Bioinformatic predictions > Coarse-grain > Protein-Nucleic > Nucleic > Ligand > Glycan > Peptide

Meaning if your system has, for example, protein-nucleic and a peptide, the protein-nucleic has higher priority than the peptide optimal parameters - and only one of these is applied.

Good to know, thanks!