Talk:Homology modelling Gaucher Disease

From Bioinformatikpedia
  • + Interesting idea to also feed Modeller with the HHSearch alignments -jonas
  • + Very neat to even let us check out the git repository with all the files (The numbering in the protocol doesn't work though?) -jonas
  • + I like that you tried to improve the model by removing uncovered regions from the alignment -jonas
  • + Very helpful to always use the same colors for the models from the different templates -jonas
  • + The short and clear conclusions are nice -jonas

  • o I would prefer am more scientific writing style without we/our but I guess it's not very important for this practical -jonas
  • o Concerning the high sequence identity template it would have been interesting to see the results on 2nt0_A, despite 100% sequence identity. Surely the structure is not completely identical and this might have had some effects on the homology modelling -jonas
  • o Shadows in raytraces of protein structures can be helpful to give perspective but I would turn them off for complete protein views, since they are more confusing than helping there (for me at least) -jonas
  • o 'Modeller failed to built a model' You mean SWISS-MODEL? -jonas

  • - 'HHsearch alignments are therefore thought to be more accurate than those produced by Modeller which should lead to better models' Makes sense, given the context given before but you make it sound like it is something well known generally. Do you have a citation on that or is it your personal opinion -jonas
  • - I like that you mostly used the same perspective for the superimposition of reference and model, however it would have been ideal to really use this all the time. I cannot compare some of the models this way and would even assume things that are contrary to whay you say, given the current figures (e.g. seems better than to me) -jonas
  • - 'Taking advantage of more than one template improves the model quality in particular if the templates cover different region, e.g. different domains, of the target sequence. However, this had not been the case for our target since 2wnw_A had already the highest coverage' Maybe I'm missing something but how do you know if it wasn't the case here? -jonas
  • - 'Segment matching vs. fragment assembly ' Not sure if this section is really necessary. If you want to keep it, I believe it would make more sense to put this to the beginning, since you are already referring to fragment assembly during your discussions. You should also add were Modeller lies here. -jonas

The text is easy to read and the important points are made clear. You could have done some more analysis but I understand not all were mandatory and we did neither. What you did, you did very well :) -jonas

There is really not much I can add :)

  • You work only with proteins <30% sequence identity. This makes the results a little less comparable to the other groups, but your protein is really well conserved and thus it all works out. You could have added the methods default modelling just for comparison.

...I found it astonishing that you got SWISS-MODEL results as we did not for the template with <30% sequence identity.

  • The text is very compact and well written! Very nice:).
  • I found merely 3 grammar mistakes: to not cover, whose comparable, a slightly model.(I listed them so you can correct them if you want, not because they are so severe)
  • I can see why you put the segment-fragment section in there, as there were some confusions among the listeners of your talk last time. I found it unnecessary that the talk was so often interrupted by the way but I don't think anyone will remember that. As there is no segment method employed in this task (or is modeller one? if so then you should put that in the method description) I think this section seems a bit out of context...... Just my opinion though

See you soon, :) Alice