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Protein Models

Posted: Mon May 17, 2021 7:03 pm
by lalghani
Hello,

I have used I-TASSER to generate protein models of Uniprot sequence - "Q9BQI3" ( job id S614180 )

the results showing TM-score 0.33 , RMSD 16.9 and C-score 3.52 for the top model.

How can I evaluate the generated model ? can I use the model for docking studies?

Re: Protein Models

Posted: Tue May 18, 2021 2:05 pm
by robpearc
In your case, it seems that the generated model had a low confidence score. The estimated TM-score is 0.33, where TM-score ranges from 0-1 and a TM-score >=0.5 is generally used to indicate that the model has the correct global fold. Of course, it is not always true that a low c-score means a poor quality model, but it is indicative of this. You may try to use the model for molecular docking studies, but the results may be questionable given the estimated model quality.

Re: Protein Models

Posted: Tue May 18, 2021 9:42 pm
by lalghani
what is the cause of the low confidence score for this model?
is it because of the low sequence identity templates used to build the model?
is there any correlation between low confidence score models and low sequences identity?