Calculation of TM-score and rmsd for all predicted models by I-TASSER

[FYaghoobizadeh]

I submitted my job on the I-TASSER server (ID ) and get the results. According to the server help page, a higher c-score (i.e., more positive) is better. Is it true? accordingly between 5 top predicted models for my structure (with C-score -2.72, -2.32, -1.20, -3.39, and -2.94) I choose the model 3 with c-score -1.20. However, TM-score and RMSD are only provided for model 1 (C-score -2.72). In this regard, I validate the structures of model1 and model3 by saves v6.0 and proSA servers and get the better results for model 3.
How could we obtain these indexes for other models? Moreover, I compared the 3d of model3 with 10-top ranked model presented in I-TASSER results page with Swiss model structural assessment tool. Is this work to calculate TM-score and RMSD OK?
I will be very thankful if you guide me as rapid as possible.
Sincerely yours

[terassda]

Yes, your understanding of the C-score is correct. The C-score provided by the I-TASSER server reflects the confidence in the predicted model, and a higher (more positive) C-score generally indicates a better model. So, choosing model 3 with a C-scoregeometry dash of -1.20 over model 1 with a lower C-score (-2.72) is a reasonable decision, especially since you've obtained better validation results for model 3 on SAVES v6.0 and ProSA.

[sabrina23]

I submitted my job on the I-TASSER server (ID ) and get the results. According to the server help page, a higher c-score (i.e., more positive) is better. Is it true? accordingly between 5 top predicted Block Blast models for my structure (with C-score -2.72, -2.32, -1.20, -3.39, and -2.94) I choose the model 3 with c-score -1.20. However, TM-score and RMSD are only provided for model 1 (C-score -2.72). In this regard, I validate the structures of model1 and model3 by saves v6.0 and proSA servers and get the better results for model 3.
How could we obtain these indexes for other models? Moreover, I compared the 3d of model3 with 10-top ranked model presented in I-TASSER results page with Swiss model structural assessment tool. Is this work to calculate TM-score and RMSD OK?
I will be very thankful if you guide me as rapid as possible.
Sincerely yours

You can use TM-align to calculate the TM-score for each of your predicted models (model 1, model 3, etc.). Calculate RMSD using alignment tools such as PyMOL or VMD if needed, comparing the predicted models to the native structure. For further validation, use ProSA or SAVES for quality assessments, as you did for model 3.