Talk:Homology-based structure prediction (PKU)

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!

source: [1]

We also want to mention our slogan for this current teamwork

criticism

• variety of methods to be used for tertiary structure prediction: I know three types: ab-initio, homology modeling, threading. What else is out there?
  • [2] mentions 4.9 mio hits so i guess there are a variety of ideas and approaches to deal with this topic. Plus [3] specifies in #3 that its a number of things 3>0 and therefore a variety--Hollizeck 21:50, 3 June 2012 (UTC)
  • a-priori
• What is the purpose of listing the results of three different search tools and not just, for instance, HHsearch?
  • isnt it surprising to you that you do not find at least a similar result when using different approaches? If i do not have a Reference to define right and wrong, how do i know which of the searchtools helps me? Plus what would you do if HHsearch has no result? And just to explain my train of thought:
    

why do i use an external program to search the pdb, if the pdb does provide one? But then if those results for the low sequence identity do have a bad e-Value, whyy dont i search with another tool to get a better dataset. BUT then this searchtool does not get any result for the middle identity section. Wouldn't you use a third tool to see if there is a explanation for this big difference in the results?

• Why do you not use common templates of different sequence identity (high, medium, low) for all three methods (Modeller, SWISS-MODEL, I-TASSER)? How will you compare the methods otherwise?
• Did you compare 2phm to 1pah? They should look identical if the sequence identity is 95%.
  • isn't that kind of our job in this Task? I mean to find out if they look identical with a high identity? --Hollizeck 21:50, 3 June 2012 (UTC)
• Figure 3: Is the blue structure actually 1pah? It looks different from figure 1 and the thread seems rather unusual.
• SWISS-MODEL finds of course 1J8U:A since the sequence identity is 100%
  • what is your point?
• There are still plenty of spelling errors.
• In the above 80% dataset we find again our structure from above. Would you write this in a paper?
  • i would not, but this is not a paper but a wiki where I can use links and references to make it more dynamic--Hollizeck 21:50, 3 June 2012 (UTC)
• You might make your plots more uniform, e.g. by using the same background color.
  • good idea --Hollizeck 21:50, 3 June 2012 (UTC)

references

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