Steven Pletsch Lv 1
How accurate do you estimate the predicted secondary structures to be ? 80% 90% 95% ? Just curious how much room there is to play with them and still remain within acceptable ranges.
1258: Tuberculosis Challenge - Phase 1
Closed since over 9 years ago
Intermediate Overall PredictionSummary
- Created
- July 11, 2016
- Expires
- Max points
- 100
This puzzle starts with an unfolded sequence with secondary structure assigned from PSIPRED. The target protein is LepB and is currently being investigated for drug discovery against Tuberculosis (TB). TB is caused by the bacillus Mycobacterium tuberculosis and has killed more than 1.5 million people in 2014. Right now, no crystal structure exists for this target. Models created by Foldit players will be used to help solve the structure when crystals become available.
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Comments
tokens Lv 1
I don't see the reason for extending the time for this puzzle. I doubt anyone will get close to anything resembling the correct fold with such little info we have been given. Rather go on to phase 2 where hopefully you will give us some more info to work with.
brow42 Lv 1
Since free_radical is being so helpful, here's my question.
There's a region i,i+4,i+8,i+11 of pro-pro-pro-xxx repeated x3 putting about 12 prolines almost colinear when in an alpha helix. Does this pattern have a particular binding partner, or would it bend the helix, and does it have a name? or does this never occur?
spvincent Lv 1
They are guidelines only and need to be taken with a pinch of salt. Sometimes when you have long helices you can be pretty confident in the prediction but if, as here, you have scattered small fragments they don't mean too much. In some predictions the results come with a percentage figure that represents the confidence but that isn't provided here. There are public servers that will let you paste in the primary sequence (as supplied by Susume in the first comment) and provide a secondary structure prediction that may be different from the one provided. Here's one:
toshiue Lv 1
the expiration time of 23:00…PDT, as usual?
Thanks
Tosh
free_radical Lv 1
This is pretty cool Jeff101 and good work. Our scientists also thought along similar lines; however -
"LepB is located in the cell wall with N-terminal at the cytosol, both are known to be reducing environments.
So, I don’t think so but there might be a part of LepB sticking out to the extracellular compartment and some of disulfide might be formed." -anonymous scientist :)
According to predictions using PSORT, it doesnt look likely that there would be any disulfides forming.
free_radical Lv 1
The predictions that I used came from PSIPRED, which I use for no other reason than it was what I was taught in graduate school. Here is the prediction that I used (edit, formating is bad. The original submission I made to PSIPRED can be found here, so everyone doesnt have to resubmit the sequence: http://bioinf.cs.ucl.ac.uk/psipred/result/4d4511ee-4775-11e6-8df1-00163e110593) :
Website: http://bioinf.cs.ucl.ac.uk/psipred/
If you would like to take a look at it.
free_radical Lv 1
Hi brow42,
I dont know the answer to this question, but I am asking around. Hopefully we can come up with one.
-free_radical
free_radical Lv 1
This is because I have only posted 1 puzzle before and I had a little trouble posting this one. I dont mind extending the time for this phase.
free_radical Lv 1
This is great information and you are on the right track!