Tertiary Structure using Avogadro

I saw in this paper that Avogadro was used to generate the tertiary structure of the ssDNA molecules. (https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/chem.202104481) My understanding was that Avogadro could not generate tertiary structures with loop structures. I am interested in using Avogadro for a similar purpose but need to understand the process and extensions available capable of doing this. Can you assist?

Thanks for the message. First off, you prompted me to finish off the “Insert DNA” command for Avo2.

You’re right that we don’t generate tertiary structure. (There was a thread here about it.)

What I’ve seen for RNAfold is that it operates from the sequence, e.g. RNAfold web server

I skimmed the paper and it seems as if they did something like this:

  • started with MD simulations of the target protein in GROMACS
  • create ssDNA strands in Avogadro
  • docked the strands using HDOCK with representative MD snapshots
  • took the top 10-scoring complexes for analysis

Given that, it’s pretty easy to create ssDNA in Avogadro. If you have a FASTA sequence, you can paste it into the “Insert DNA/RNA” window and pick the parameters (notably the “single strand”).

Hope that helps!