Hi, I'm Meechl. Welcome to my wiki page!
R scripts (wiki page on how to use R scripts)
While working on labs a few days ago, for some reason I decided that I needed to know the best tetraloop structure. So, I attempted to find out by looking at past lab results. So far, my data includes Cloud labs 0, 69, 71, 72, 73, and 74. In total, I scored 7,032 tetraloops. (I didn't score the barcode.) 4,132 may seem like a lot, but when you consider there are 4096 possible tetraloops... not so much. The vast majority of possible tetraloops were not tested at all.
I score each tetraloop out of 100 based on the SHAPE score of each base. Closing bases got credit for having reactivities <0.75 and the bases in the loop got credit for having reactivites >0.25. For each type of tetraloop, I found the average score.
These are the scores of the tetraloops with at least 10 trials:
And... They all scored pretty well. (AAAAAU is a possible exception). The results used to look more exiting (varied) before I found an error in my calculations. :(
I still haven't taken out data with lots of error, or checked to make sure I haven't made any more errors.
Scores for all designs in Cloud Lab 70 (unbound vs bound w/ FMN. Mimic Structure = Target FMN Bound Structure):
Data from Cloud Lab 70:
Graphs comparing the data between switches using FMN and a mimic sequence:
Attempts to score the switches:
My Current Switch Score Guidlines (See Brourd's and my talk for discussion):
- Bound state is defined as the mimic structure
- All bases with shape data are scored (79 total)
- Each base can score MaxReward(5), ReducedReward(3), MinReward(1), or zero
- Sum of scores for each base is divided by highest possible score to get the final score shown in the google doc
- A base is considered paired if SHAPE reactivity is <0.5 and unpaired if >0.25
Table of how bases were scored. Cases not listed in table scored 0.
|Target Shape of Unbound||Target Shape of Bound||SHAPE reactivity of Unbound||Shape reactivity of Bound||Score|
|Paired||Unpaired||<0.5||>0.25 (and at least 0.25 > unbound)||MaxReward|
|Paired||Unpaired||any||at least 0.25 > unbound||ReducedReward|
|Unpaired||Paired||>0.25||<0.5 (and at least 0.25 < unbound)||MaxReward|
|Unpaired||Paired||any||at least 0.25 < unbound||ReducedReward|