Talk:Glucocerebrosidase homology modelling

From Bioinformatikpedia

Very nice report!

Some comments to think about:

  • an RMSD of 1.9 A between the apo and a complex reference structure seems higher than expected for me. Do you know where the big differences are?
  • It's interesting that Modeller messed up the secondary structures for the mixed templates. Are the templates so different? Didn't it manage to align them in 3D?
  • Did you notice that the TM-score of the combined model is also better than the the on of the 2E4T model alone?
  • Modeller also gives a numeric score for its models (DOPE). Did you check that? Does that score correlate with the model quality?
  • What is the contribution of the second template in iTasser? I.e. which part of the sequence is modelled with the second template? Why does this improve the TM-score compared to the Modeller models?
  • The binding site RMSD of the iTasser model is also remarkably good. Can that be explained by the second template?

Edit [Tatjana]:

  • It seems that there had happened a mistake while calculating the RMSD between the apo and the complexed reference structure, so it was calculated again: in reality is is only 0.2 Angstrom.
  • DOPE was added to the modeller results