Peptide nucleic acids

HADDOCK
1

Hello all,

I hope you are doing great.

I am planning to dock peptide nucleic acids (PNAs) into a protein. Is it possible to dock PNAs (~20 bases) in the form of single stranded or RNA-PNAs hybrid or double stranded PNAs?

Thank you in advance.

Jameel

2

We don’t have support for PNAs unfortunately

4

Sorry for any incovenience caused Prof. Bonvin.

The parameters for PNA are currently included in CHARMM36m force field. Is it possible for PNA to be included in HADDOCK’s library as a group of modified nucleic acid? Or the user can provide a parameter file and treat the PNA as a ligand with HETATM record?

5

The parameters for PNA are currently included in CHARMM36m force field. Is it possible for PNA to be included in HADDOCK’s library as a group of modified nucleic acid? Or the user can provide a parameter file and treat the PNA as a ligand with HETATM record?

The server does not allow to upload parameter files.
You might try to include those in a local version of HADDOCK (and make sure all runs fine).
If you manage we can then include it in the server version :slight_smile: