Tertiary Structure using Avogadro

General Discussion
1

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?

2

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!