Talk:Task 4: Homology-based structure prediction

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Revision as of 23:41, 4 June 2012 by Hollizeck (talk | contribs)
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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 structure"-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 simple 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 (see <xr id="fig:model1dwt1qs0hollizeck" />

<figure id="fig:model1dwt1qs0hollizeck">

model (red) and reference(green) superimposed

</figure>

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