Why was the base mutation constraint for the TEBOWNED labs set at 8?

  • 1
  • Question
  • Updated 6 years ago
  • Answered
In regards to the 3 new TEBOWNED labs, why was the base mutation constraint set at 8, and not 7, or 9, or 5? Should we be aiming for solving the structure with as few mutations as we possibly can?
Photo of Brourd

Brourd

  • 446 Posts
  • 82 Reply Likes

Posted 6 years ago

  • 1
Photo of tsuname

tsuname, Alum

  • 12 Posts
  • 2 Reply Likes
Hi Brourd, thanks for looking into the TEBOWNED structure puzzles!

Should we be aiming for solving the structure with as few mutations as we possibly can?

Yes, that's exactly it. We set the limit to 8 mutations since this is the most number of mutations that I have used to stabilize a particular structure, so it it kind of an "empirical" upper bound. I'm pretty sure that given your experience, you guys can probably do better ;)
Photo of xenosapien

xenosapien

  • 7 Posts
  • 0 Reply Likes
Oops. I might need to go back then. Since we had a budget of 8 changes, on at least one of the puzzles I used the "extras" to play with the dot-plots. I think I'd gotten one done with just 2 (maybe 3) tweaks, but then I kept tweaking it to use my "budget".

Oh well, live and learn.
Photo of tsuname

tsuname, Alum

  • 12 Posts
  • 2 Reply Likes
@xenosapien

I see, it's definitely not clear that the less mutations you use to stabilize a structure, the better. I'm going to try get the description of the challenge updated, thanks for the input!
Photo of Brourd

Brourd

  • 446 Posts
  • 82 Reply Likes
Did the Das lab happen to synthesize the original TEBOWNED design using the new synthesis protocols to allow players to compare its chemical footprint to those of the 48 new mutants? I would be greatly interested in seeing the results for the original design with both +/- FMN conditions using the new protocol.
Photo of Brourd

Brourd

  • 446 Posts
  • 82 Reply Likes
Aha, I just checked the RMDB entry for round 72, and it looks like there are entries for the original sequence and some mutation/map designs.
Photo of Brourd

Brourd

  • 446 Posts
  • 82 Reply Likes
Is there any chance we will see the entries for the mutation/map run on TEBOWNED in the game itself any time soon?
Photo of tsuname

tsuname, Alum

  • 12 Posts
  • 2 Reply Likes
Hi Brourd,

We did run mutate-and-map on TEBOWNED in this (round 72) cloud lab. As you already noticed, the data can be found in the RMBD here; the name of that project is "TEBOWNED reloaded". You can also find the data for the eterna puzzles challenging to stabilize each of alternative states (TEBOWNED U, B, and BH for (FMN) unbound, bound, and bound + extra hairpin respectively).
I'll ask Jee to see when the data is going to be posted in-game.
Photo of eternacac

eternacac

  • 274 Posts
  • 19 Reply Likes
I found the nucleotide limit to be unclear as to intent and so ultimately discarded a one nt and several low nt solutions to improve dot plot as mentioned above. Maybe a minimum needed to stabilize challenge should be specified?