You are here

How can I model ligands in comparative modeling

2 posts / 0 new
Last post
How can I model ligands in comparative modeling

I need to model a protein with multiple chains and have found several templates for comparative modeling. I want comparative modeling to output a structure that has a ligand binding with it, and I've noticed at the bottom of the tutorial that after adding the tag use_hetatm=1 to my xml file, any ligand that I want to model with will be taken from all templates with non-zero weight. The tutorial also emphasizes that ligands must be added to all templates with non-zero weight in the xml file, but one of the templates I'm using contains no ligand. That structure is a necessary template and I can't build my model without it. Is there any suggestion about how to model the ligand in this situation?

Post Situation: 
Thu, 2020-02-20 09:57

This answer depends on how different the ligand binding sites are between the homology models, but you could align the homology models in pymol, and then copy the ligand from one of the other models into the structure of the ligand-less model.


If that's impossible, you can try some complicated manual modelling with hybridize by frankensteining parts of the structure you want onto a structure that has a ligand.  but that can be quite complicated and time consuming, and i'm not aware of any publications or protocols that do that without extra information like electron density.  But you could be the first if it works!

Fri, 2020-02-21 17:05