Protein Models

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lalghani
Posts: 2
Joined: Mon May 17, 2021 11:05 am

Protein Models

Post 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?
robpearc
Posts: 40
Joined: Sun May 02, 2021 5:49 pm

Re: Protein Models

Post 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.
lalghani
Posts: 2
Joined: Mon May 17, 2021 11:05 am

Re: Protein Models

Post 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?
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