Docking Pyroglutamic acid (or non-proteinogenic amino acids)

HADDOCK
1

Dear HADDOCK team,

I am searching for a possibility to run a docking (easy interface web server) on a ligand that contains a non standard proteinogenic amino acid, to be precise it is the matter of Pyroglutamic acid.

When performing the docking on a structure containing Pyroglutamic acid, HADDOCK converts the pyroglutamic acid back to standard glutamic acid (but nevertheless successfully finishes the run).

Considering the modified amino acids that HADDOCK recognizes (see haddock.science.uu.nl/services/HADDOCK/library.html), pyroglutamic acid is not listed.

Regarding the PDB format, pyroglutamic acid differs from standard glutamic acid only by the absence of the ATOM line “3H”, which is strangely anyhow not listed in the above-mentioned link.

Is there a possibility to add pyroglutamic acid to the list of amino acids recognized by HADDOCK (preferably in the web server, or alternatively for a locally installed version) ? Or can anybody add pyroglutamic amino acid to the ones that are recognized by HADDOCK?

Many thanks in advance for your support!

2

It is more than just an atom difference, the chemistry is different. Needs to be parametrized and properly tested. Not so simple.

Also the reported names are the one used by HADDOCK and the force field used. Missing atoms will be generated automatically.