Call for HARD lab puzzles that can fail automated algorithms

Dear all -

We are planning to perform a large scale evaluation of the “EteRNA ensemble algorithm.” - Specifically, we want to test the algorithm on lab shapes that other automated algorithms such as ViennaRNA and NUPACK will fail!

We’ll synthesize 12 designs for each puzzle - 4 by NUPACk and 4 + 4 by 2 different versions of EteRNA ensemble algorithms, and we want our players to pick the shapes!

Please write down the puzzle you would want to test the automated algorithms - Again, please note that we are looking for hard cases where algorithms would normally fail and want to see if EteRNA ensemble algorithm can make an improvement!

You can find the list of lab shape candidates here.

We are looking forward to seeing exciting shapes from players.

EteRNA team

I would love to pick Brourd’s Big loop, as it is particulary evil. But there is a new untested element in it - the big loop - so I pick Quasispecies Water strider instead.

I’d go for fractile or hard Y and a bit more


Yes, please. Fractile.

  1. “Big Loop” or “A Loop and a Branch”
  2. “Energy Test”

I like “hard Y and a bit more” and “kudzu” … but since one of mine has already been chosen I’d particularly like to see Hard Y.

Forget bots… that puzzle gave a certain human problems the first time through.

For now, my vote is for “Shapes and Energy” or “Energy and Shapes”

I would like to see hard y and a bit more too