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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... ?
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?
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
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?
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Such a concise but informative video. Thank you
Glad it was helpful!
This is helping me a lot for my research, thank you very muchhh
Glad to hear that!
You have made learning a fun and easy task for us, Sir. Really appreciate the effort. :)
It's my pleasure
Thank you for all your efforts💫
Obliged
sir you have made it easy..
thanks Hamza
Very helpful tutorial 💯
Glad you think so!
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?
Hi, Hope you have enjoyed our Bioinformatics videos. Now DataScience & Bioinformatics Team is inviting you to attend an Excellent Course to Learn Complete Bioinformatics from Scratch on Discounted Prince. After taking this course, you will be very confident and we ASSURE YOU THAT THIS GAME CHANGER FOR YOU.
There are details about the Theory and Practical of
Homology Modeling
Threading, 3D Structure Prediction
Evolutionary Bioinformatics
Gene Predictions
Database Searching
Alignment
Docking
and everything you can expect. So what are you waiting for? Please click below to get the course at a discounted price.
www.udemy.com/course/learn-bioinformatics/?referralCode=35C6DA89E7B61CA56DCC
Amazing
Very informative..👍
Many thanks
Hi, is it necessary to perform energy minimization with ITasser models or they are already energy minimized?
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... ?
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
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?
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
@@bioinfoxpert so should i try AlphaFold also?? I was thinking to refine ITasser models with GalaxyRefine.
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
@@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
Use interrpro, it will not only let you know the domain but also about domain structure available in pdb
How much time will it takes to recieve our model
Dear It depends upon the server availability. Norammly, people receive the results in 48 hours.
👍
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?
Sir mere result main graph nhi aya,sir KIA maira result accurate hai?