3D shape(s) of your Pseudoknots?

Hi! Wondering if there’s a convenient tool to visualize the 3D shapes of pseudoknots. A way that lets you explore the parts’ range of motion. Must be some tool like that - it seems like a generally important thing!

Many of our puzzle have Eterna3D representing the structure reported in a PDB file by researchers. The puzzles in OpenKnot round 6 have an Eterna3D structure except the for the last one, which is Roll Your Own Pseudoknot. The 3D tool most commonly used by Eterna players is Chimera.

I’m not aware of a 3D visualization tool that switches between different states. Modeling 3D is still such an uphilll climb that researchers aren’t talking about representing the different states yet, plus it would require a large amount of computation.

A unique aspect of RibonanzaNet is the reactivity prediction that potentially will reflect the ensemble of conformations rather than only one. I’ve suggested to the Das Lab that a new Kaggle challenge could provide all the reactivity reads in the training set with the goal of predicting multiple states.

If you have a pseudoknot that you believe has an important range of motion, please share!

Thank you DigitalEmbrace! I wonder if these apps are easily accessible and user-friendly, yet. Meanwhile I want to share this physical building toy that seems ideal for visualizing and manipulating pseudoknot structures and their dynamics…
See here: https://youtu.be/i2QfKlvkE4s
And eterna-themed kits (32nt) are for sale here: eteRNA-themed building kit — TeachDNA