Generate Protein

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Edward Pullen
Posts: 3
Joined: Fri Jul 09, 2021 5:23 am

Generate Protein

Post 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!
robpearc
Posts: 42
Joined: Sun May 02, 2021 5:49 pm

Re: Generate Protein

Post 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.
Edward Pullen
Posts: 3
Joined: Fri Jul 09, 2021 5:23 am

Re: Generate Protein

Post by Edward Pullen »

Please advise how can I improve TM-Score to 0.5?
xiaogenz
Posts: 139
Joined: Sun Apr 25, 2021 12:02 am

Re: Generate Protein

Post by xiaogenz »

You can try to provide the template and distance restraints.
JohnAlvarado
Posts: 1
Joined: Mon Oct 18, 2021 7:21 am

Re: Generate Protein

Post by JohnAlvarado »

Is it really beneficial?
xiaogenz
Posts: 139
Joined: Sun Apr 25, 2021 12:02 am

Re: Generate Protein

Post 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/
John_wick
Posts: 1
Joined: Mon Mar 28, 2022 3:21 pm

Re: Generate Protein

Post by John_wick »

How does DNA turn into protein?
Last edited by John_wick on Wed Mar 30, 2022 12:37 pm, edited 1 time in total.
zcx@umich.edu
Posts: 24
Joined: Wed Nov 03, 2021 5:59 pm

Re: Generate Protein

Post 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.
Mifuko
Posts: 1
Joined: Mon Mar 14, 2022 4:20 pm

Re: Generate Protein

Post 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.
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