Zhanglab forum

I submitted a job to your server (Job ID: [insert ID]) and reviewed the five predicted models. I selected Model 3 (C-score: -1.20) for further validation since it has the highest C-score. However, TM-score and RMSD values are only provided for Model 1.

I validated Model 3 using SAVES v6.0 and ProSA, which showed better results than Model 1. I also compared Model 3 to top-ranked models using the SWISS-MODEL assessment tool.

Could you please advise:

How can I obtain TM-score and RMSD for the other models (especially Model 3)?

Is it acceptable to calculate these values using third-party tools like SWISS-MODEL?

Thank you for your help!

Best regards,

The TM-score shown on the I-TASSER results page is not an actual TM-score, but an estimated value based on simulation parameters. We only provide this estimated TM-score for model 1, as the estimates for other models are less reliable. If you still wish to obtain an estimated TM-score for other models (e.g., model 3), you may use the value from model 1 as a rough approximation.

You cannot calculate the TM Score and RMSD for Model 3 if you only have the model file and no reference structure to compare to.

You can calculate TM-score and RMSD for your other predicted models by downloading their PDB files from I-TASSER and comparing them using the TM-align tool. Simply run TM-align between each predicted model and the reference structure to get TM-score and RMSD. Using third-party tools like SWISS-MODEL or ProSA is also acceptable for cross-checking, as long as you mention it in your methods section.