Difference between revisions of "Talk:Task 4: Homology-based structure prediction"

Revision as of 22:27, 4 June 2012

Well, I can see you have some bad luck with your protein, but still some comments so far:

You could have tried, what i-tasser does, if you exclude homologous templates (option II, cut-off).
Pictures of the models and maybe a table collecting the scores of different methods for the same template would give a better impression

Boidolj 17:03, 4 June 2012 (UTC)

I must say i am rather surprised about your results, in addition to what Jonathan already told you above i have some other issues:

if you couldnt find anything with Coma and HHPred, why dont you use another searchtool?
why do you exclude the 99% identity candidate? If we assume the "I dont't know my proteins tructure"-case and you find a hit with 99% identity you would use it wouldnt't you? So why exclude a structure of a slightly changed protein especially if you dont have any other?
why do you assume that it is a problem that your 1qs0 hit is from bacteria? I thought this Task is about finding conserved regions, because we assume they have the same structural conformation. And that would include cross-organism-hits as well from bacteria as from mammals or anything else
why do you have doubts which model to choose for the 30% identity part? isn't the choice just simpel using the hit with the best e-Value?
with your I-Tasser result i am quite surprised, because if i have a look at the models they seem to be very conserved and even the scores (apart from your tm-score) suggest a very good model. Especially the tm-score calculated by I-Tasser (0.69+-0.12) is very good

--Hollizeck 21:27, 4 June 2012 (UTC)

@@ Line 5: / Line 5: @@
 [[User:Boidolj|Boidolj]] 17:03, 4 June 2012 (UTC)
+I must say i am rather surprised about your results, in addition to what Jonathan already told you above i have some other issues:
+* if you couldnt find anything with Coma and HHPred, why dont you use another searchtool?
+* why do you exclude the 99% identity candidate? If we assume the "I dont't know my proteins tructure"-case and you find a hit with 99% identity you would use it wouldnt't you? So why exclude a structure of a slightly changed protein especially if you dont have any other?
+*why do you assume that it is a problem that your 1qs0 hit is from bacteria? I thought this Task is about finding conserved regions, because we assume they have the same structural conformation. And that would include cross-organism-hits as well from bacteria as from mammals or anything else
+*why do you have doubts which model to choose for the 30% identity part? isn't the choice just simpel using the hit with the best e-Value?
+*with your I-Tasser result i am quite surprised, because if i have a look at the models they seem to be very conserved and even the scores (apart from your tm-score) suggest a very good model. Especially the tm-score calculated by I-Tasser (0.69+-0.12) is very good
+--[[User:Hollizeck|Hollizeck]] 21:27, 4 June 2012 (UTC)