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?
• 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.