Talk:Structure-based mutation analysis (PKU)

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This is just a place to add criticism and or positive feedback so we Jonathan and Sebastian have a possibility to improve. Please note, that we wont be able to adress all matters immediately but we will address them eventually!

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source: [1]


positive feedback

Again, everything very nice !--Meiera 23:51, 25 June 2012 (UTC)

  • Thanks for teaching me the word 'malign', I only knew malignant :) -jonas


  • What exactly do you want to convey by "...left for the reader as exercise"?
    • yeah, kinda hard to compare the two figures. You should have enough colours for all three ;) -jonas
  • The SCWRL and FoldX energies (-> tables) could use some elaboration but you already know this.
  • Very wild color :)..... a overall color-scheme could make the entry more straightforward

das wars von mir, gute nacht --ali

  • 'the color is chosen automatically by PyMol'. This is a bit confusing, why not always colour the structures the same? -jonas
  • You might have focussed too much on only the change of hydrogen bonds. What about clashes to neighbouring atoms, introduction or removal of charged residues that might have coorindated other charges nearby. What about things like pi-stacking, the possibilities are endless ;) -jonas
  • I like how much emphasis you put on the surface considerations, however it felt like there was always the final step missing. You describe that e.g. there is a buldge created but what I really want to know in such a case is what is the effect of this. Is the binding pocket changed, is it at an interaction site (you have a multimer iirr), what about the case where a charge is removed from the surface. You would think there might be a reason if a strong charge is placed standing out on the surface. I am very much aware though that information like this is really hard and time-consuming to find. -jonas

Small stuff

  • 'SCWRL forms a bond (colored in blue)': What do you mean? A hydrogen bond? Then I don't see it. Or the additional atom at the backbone? That should be simply a hydrogen added by SCWLR, right?
  • 'Our journal might be found here' Are you just being really polite towards the reader or does the journal sometimes not feel like it and then disappears? ;)
  • Suggestions for conclusion if you change your mind ;): FoldX or SCWRL? Correlations of energies, benefit of minimize, effect of different force fields...
  • 'Again the changes seem to be rather big, but there are no visible changes in the bonds or clashes ' What do you mean then by the big changes? Changes in the global structure? How can you know this, looking only at the figure, a strong effect is not immediately apparent.
  • You might put some of the values from the Gromacs section like average changes in a table, so they are easier to compare without jumping between breaks


urgent matters

Just noticed that you used charmm27. When you use this force field the output from g energy misses angles. Also the number of the potential attribute is shifted 1 is Bond, 2 is "U-B" and 12 is "dont know right now". The potential is number 13. Im not sure what exactly U-B is but i think angle would be given when choosing the attributes Joerdensv

  • Ahead of you: Fixed the potential energy, still trying to figure out the "angle" option. Thx anyway! Boidolj 14:14, 24 June 2012 (UTC)