Difference between revisions of "Task 6: Protein structure prediction from evolutionary sequence variation"

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Revision as of 18:38, 22 August 2013

Results

lab journal

Contact Prediction

<figure id="ras_score_dist">

Cn score ras.png

</figure>


<figtable id="hfe_score_dist" align="right">

Cn score imm.png
Cn score mhc2.png

</figtable>


<figure id="cm_1a6z">

ContactMap 1a6z new.png

</figure> <figure id="cm_hras">

ContactMap 5p21.png

</figure>

  • Why are the scores of residues close in sequence amongst the highest? Why are the pairs distant in sequence (n>5) more interesting for structure prediction?
  • Look at the values, range and distribution of scores.
  • How many of the high-scoring pairs are true or false positives? Does this correlate with the value of the score? Visualize the predicted contacts together with the crystal structure contacts in a contact map plot.
  • Can you determine evolutionary hot spots, i.e. functionally important residues? Compare to conserved sites in the MSA. Compare with your results from task 7 (when you are working on task 7, i.e. this is a task for the future).
  • Here, the DI score is given. Compare the top 50 DI and CN (from freecontact) scores. How large is the overlap (>80%)?

MHC EVFOLD: constraints: 70(40%) 113(65%) 174(100%)

imm EVFOLD


RAS EVFOLD: 189 / 160 189: 76 (40%) 123 (65%) 189

Discussion