Amino acid-nucleotide preferences

The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab


Does HADDOCK have an algorithm that specific amino acids have preferences for specific nucleotides (for instance lysine prefers binding to adenine) in protein-DNA docking? Is there relevant literature to point me to for this?

No there is no such potential in HADDOCK

You could in principle define ambiguous restraints for this.

But my impression is that specific aminos actually do prefer specific nucleotides in nature (ie. Luscombe et al. 2001)? If so, I find it strange that HADDOCK does not account for this.

If you have a set of orthologous proteins that bind slightly different DNAs, I was thinking that these preferences may be used to infer the amino acid-nucleotide pairings.

Any preferences observed could be encoded as ambiguous restraints in principle.

I would find it dangerous to make it systematic as these remain “preferences” and not physical rules.

Hi again, thanks for the answer. And I agree with you, it seems spurious to make it very systematic.

I have a very different question though. HADDOCK seems to strip almost all hydrogens from the amino acids in my proteins when docking protein-DNA. For instance, in my input protein, Trp has 11 hydrogens, but in the final models it is left with only three. Why?

By default we only keep the polar hydrogens so save computing time.

But there is an option to keep them all (docking parameter tab)