Hi, thank you again for the powerful tools.
I have got my first results from I-Tasser (Job ID: S133387). I am very confused about these questions:
1. I-Tasser supplies 5 models for protein, and from the scores I know the first one is the best. I wonder: is there a criterion to evaluate the reliability of the model? Such as, when C-score>0, the model is reliable and we can use for docking or something else.
2. Top 10 templates used by I-TASSER are listed. I also used the blastp in RCSB, and I just found 1V65. As we know, homology modeling can be done when the similarity between query sequence and template is >30%. So which parameter from I-Tasser represents the similarity, Iden1 or Iden2? And I feel 2b9eA is not so close to the query sequence (Norm. Z score <1), should we still use it as a template? Is there a criterion for choosing the template?
3. For the alignment, I have seen rank2, rank5 and rank7 are identical. How does I-Tasser select the top 10 templates? which parameter is critical? If there are some other crystal structures of homologous proteins, will they be missed because of these duplicated results?
4. Could I input several specify templates? Because I can just find some fragment structures from RCSB for my protein. Can I input them for one time?
Thank you very much and looking forward to your kind reply!