Generate Protein

[Edward Pullen]

Hi Everyone,
I am using I-TASSER to generate protein models of Uniprot sequence and the the results showing TM-score 0.29 , RMSD 15.7 and C-score 3.42 for the top model.
How can I evaluate the generated protein model? Please advise!

[robpearc]

Generally, a TM-score >=0.5 indicates that a protein has the correct global fold. Thus, in your case, the model seems to be low confidence. However, this is an estimation based on our statistics and may not reflect the actual TM-score.

[Edward Pullen]

Please advise how can I improve TM-Score to 0.5?

[xiaogenz]

You can try to provide the template and distance restraints.

[JohnAlvarado]

Is it really beneficial?

[xiaogenz]

Is it really beneficial?

Yes, absolutely. You can try to use our newest version D-I-TASSER, which uses deep-learning restraints to guide the modeling.
https://zhanggroup.org/D-I-TASSER/

You can also use our deep-learning based platform I-TASSER-MD for the multi-domain protein structure prediction.
https://zhanggroup.org/I-TASSER-MD/

[John_wick]

How does DNA turn into protein?

[zcx@umich.edu]

If the DNA contains an ORF, you may use ExPASy translate (https://web.expasy.org/translate/) to obtain the translated protein sequence from DNA. If your DNA is in NCBI, it should have annotations of translated protein sequences in its GenBank format.

[Mifuko]

Is it really beneficial?

Yes, absolutely. You can try to use our newest version D-I-TASSER, which uses deep-learning restraints to guide the modeling.
https://zhanggroup.org/D-I-TASSER/

You can also use our deep-learning based platform I-TASSER-MD for the multi-domain protein structure prediction.
https://zhanggroup.org/I-TASSER-MD/

Thank you for the links, really lots of useful information. I will look at both links closely later this week when I get back to my property in Istanbul.