[modeller_usage] Restraints to apply for nucleic acid

Hello!

Modeller has been quite successful at modelling my protein of interest and I am very happy with the results. I am now using Modeller to model my protein in complex with a nucelic acid (tNRA), as there is a homolog complex of known structure.

The family of models I obtained is quite good but the nucleic acid seems a little out of shape. It looks like some of the base pairing and/or stacking has been lost.

I have been thinking of adding restraints to the modelling process.

Do you have any ideas on the best type of restraints to use (H-bonds, distance, etc.)?

Thanks!

-Charlotte Habegger-Polomat, Quebec