Bioinformatics |3D Protein Structure Prediction |I-TASSER Result Analysis of Protein Structure

[@bioinfoxpert]

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[@firnaalkareemah1711]

This is helping me a lot for my research, thank you very muchhh

[@bioinfoxpert]

Glad to hear that!

[@mehwishahsan2194]

Such a concise but informative video. Thank you

[@bioinfoxpert]

Glad it was helpful!

[@sahershahid4735]

Hi, is it necessary to perform energy minimization with ITasser models or they are already energy minimized?

[@tashifaamjid5583]

Thank you for all your efforts💫

[@bioinfoxpert]

Obliged

[@sms861]

good explanation. i would like to know on what basis the 5 predicted models are ordered. is the best one is first or we should select by C score?

[@bioinfoxpert]

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[@hamzatahir2319]

sir you have made it easy..

[@bioinfoxpert]

thanks Hamza

[@DDarleenL]

Thank you for this video! It was very helpful. Although, I have a question: all the ten templates are used combined to create the top five models? or just the number 1 template is used to create the number 1 model and so on... ?

[@bioinfoxpert]

I-TASSER is based on threading. In homology modeling one template is used while in threading all best templates are considered to build best models

[@maryamjunaid2141]

You have made learning a fun and easy task for us, Sir. Really appreciate the effort. :)

[@bioinfoxpert]

It's my pleasure

[@shazminasajjad8489]

Very helpful tutorial 💯

[@bioinfoxpert]

Glad you think so!

[@harisjan6047]

Hi my protein sequence is long more than 3000, while there is limit of 1500 in I taser, if I run divide them and run half of them in each run , is it possible to link them?

[@zainiiBee]

My query sequence showed 37 percent similarity so homology modelling cannot be done. I tried to go for I-Tasser and TrRosetta. Both showed different protein structures. What should i do now? what should be my next step? please guide me Also the structures in Ramachandran plot showed less than 90% accurate residues and showed 86%. which means the structure is not validated. Now what?

[@bioinfoxpert]

Dear Zainab, you raised a very valid point. Normally people leave it unattended. Currently, alpha fold has 90% correct prediction accuracy. I-TASSER and alll other have 45% accuracy. It means that if you are using I tasser or TR roessta then you should expect error. The ideal way to get good idea about structure accuracy is to get idea about the potential domains of protein and then look at the individual domain structure in your predicted model. You can use InterPro or UniProt to get idea about potential domains in your proteins and their structurs

[@zainiiBee]

@@bioinfoxpert so should i try AlphaFold also?? I was thinking to refine ITasser models with GalaxyRefine.

[@bioinfoxpert]

Zainab alpha fold is not available yet. There will no benefit to refine the structure. I will recommend you again to check the domains individually

[@zainiiBee]

@@bioinfoxpert thank U. I am trying to loof for domains as well .. its showing 3 domains. How to get idea of their structures i am confused

[@bioinfoxpert]

Use interrpro, it will not only let you know the domain but also about domain structure available in pdb

[@shahzinakomal1675]

Very informative..👍

[@bioinfoxpert]

Many thanks

[@shanmadusanka5700]

How much time will it takes to recieve our model

[@BrinkofKnowledge]

Dear It depends upon the server availability. Norammly, people receive the results in 48 hours.

[@Islamic_insight552]

Sir mere result main graph nhi aya,sir KIA maira result accurate hai?

[@mohm3057]

Amazing

[@Islamic_insight552]

👍