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Generate Protein

Posted: Fri Jul 09, 2021 5:42 am
by 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!

Re: Generate Protein

Posted: Fri Jul 09, 2021 7:27 am
by 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.

Re: Generate Protein

Posted: Sat Jul 10, 2021 7:49 am
by Edward Pullen
Please advise how can I improve TM-Score to 0.5?

Re: Generate Protein

Posted: Sat Jul 10, 2021 4:05 pm
by xiaogenz
You can try to provide the template and distance restraints.

Re: Generate Protein

Posted: Mon Oct 18, 2021 7:22 am
by JohnAlvarado
Is it really beneficial?

Re: Generate Protein

Posted: Mon Oct 18, 2021 7:29 pm
by xiaogenz
JohnAlvarado wrote: Mon Oct 18, 2021 7:22 am 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/

Re: Generate Protein

Posted: Mon Mar 28, 2022 3:28 pm
by John_wick
How does DNA turn into protein?

Re: Generate Protein

Posted: Tue Mar 29, 2022 5:30 pm
by 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.

Re: Generate Protein

Posted: Wed Mar 30, 2022 9:39 am
by Mifuko
xiaogenz wrote: Mon Oct 18, 2021 7:29 pm
JohnAlvarado wrote: Mon Oct 18, 2021 7:22 am 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.