Support for non standard amino acids

[lightdock]

Support for non standard amino acids

[alchemistcai]

The framework of lightdock supports non-standard amino acids in theory.

It needs scoring functions designed for non-standard residues and structure recognization for them,though.

I suggest haddock if you urgently need non-standard amino acid support in protein-protein/peptide/ligand docking works.

Here are some non-standard residues it supports now.

Here is a tutorial of haddock,which alters a histidine into a phosphorylated histidine.

By the way,haddock utilizes an computational engine called CNS to treat non-standard structures.If you need more radical modifications that are out of support lists,you can ask haddock's community for help.

Rosetta,as a powerful suit for protein designments,may also support this.However,I haven't use Rosetta before,I can't give more detailed information.

Hope this helps you.

[brianjimenez]

To add on top of @alchemistcai 's response, you can always manually add new atom types and residues to some of the supported scoring functions without re-parametrizing. A good example is in the cpydock scoring function where the AMBER94 force-field is internally used and it is possible to easily add or modify types on the Python files:

• https://github.com/lightdock/lightdock/blob/master/lightdock/scoring/cpydock/data/amber.py
• https://github.com/lightdock/lightdock/blob/master/lightdock/scoring/cpydock/data/solvation.py
• https://github.com/lightdock/lightdock/blob/master/lightdock/scoring/cpydock/data/vdw.py