Difference between revisions of "Talk:Homology-based structure prediction (PKU)"

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(criticism)
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==criticism==
 
==criticism==
 
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* ''variety of methods to be used for tertiary structure prediction'': I know three types: ab-initio, homology modeling, threading. What else is out there?
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* What is the purpose of listing the results of three different search tools and not just, for instance, HHsearch?
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* 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?
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* Did you compare 2phm to 1pah? They should look identical if the sequence identity is 95%.
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* Figure 3: Is the blue structure actually 1pah? It looks different from figure 1 and the thread seems rather unusual.
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* SWISS-MODEL finds of course 1J8U:A since the sequence identity is 100%
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* There are still plenty of spelling errors.
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* ''In the above 80% dataset we find again our structure from above.'' Would you write this in a paper?
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* You might make your plots more uniform, e.g. by using the same background color.
   
 
==positive feedback==
 
==positive feedback==

Revision as of 22:12, 3 June 2012

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!

schematic group of people coloured in several colours with speech bubbles above their head
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?
  • What is the purpose of listing the results of three different search tools and not just, for instance, HHsearch?
  • 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%.
  • 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%
  • 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?
  • You might make your plots more uniform, e.g. by using the same background color.

positive feedback

suggestions