Great video. My final year research project in bioinformatics is on endometrosis, I'm very confused about my topic. I don't know how to do research in bioinformatics. This is my first Project.
Can you please upload a version of this video that does not have a background music? I feel that your content is very good, I just cannot focus because of the music. Please? Thanks in advance!
very informative and detailed explanations. I need one help. For hematopoietic CD34 protein, when I am searching for similar pdb structure by using of FASTA sequence, no result is coming. In your video(11:40-12:20), you have shown if we have partial structure also, we can make it by modeler. But if we do not get any similar structure what will be the alternative step? Can you please help me?
The video was very helpful. I have a doubt to ask Professor. When we look for the matching temple sequences and get 60 % identity with only a single target hit in BLASTP and it covers only the C-terminal region of the target, can the N-terminal be designed by ab inito methods like I-TASSER?
Thanks for your lovely tutorial, do you have concluding aspect on how to use this on modeller?. If not it would be nice to see the complete tutorial with modeller
What is the correct extension of saving the pir alignment file, " .ali " or " .ali" "? whenever I save my file with " .ali ", it gets saved as a text file. What shall I do?
Hi thank you for the lovely tutorial. I have a question, if I have an unknown sequence, can I directly use it for blastp or do I have to search for sequence homology with blast first? Thank you
Hi Sir, I would like to ask. When I edit the PDB of the template sequence, I realized there is "Connect" data after the Hetatm. Should I remove it or keep it the way it is? Thank you sir
use similar steps ... but instead of model-multiple file u have to use model-defult.py file u can get that from this folder C:\Program Files\Modeller9.24\examples\automodel\model-default.py
Hello and thank you for such a wonderful tutorial. I recently started learning Homology Modeling and I would be grateful if you help me understand this: in 17:42 you said that, in rcsb we have to check for available chains and then remove other chains in pdb file. why we have to do this? because we can define chains in modeller. we have to do such thing for all proteins when we are working on a homology modeling project? please say something here or share a link if it is possible. thanks again for your videos.
Your videos are very good, they help a lot, thank you! I have a question about the alignment. Is the alignment made by the Modeller program not the best option? Do you prefer to use ClustalW? Is there a reason? Another question is about the query sequence, is there a problem removing the amino acids that are not covered by the template before running the modeling? Could this change anything in the modeling and validation process and in the results? Thank you!
1. U can use other alignment tool, u can check my video on HH Pred tool 2. if u dont remove missing aa from sequence, the program unable to find the structural conformation of the specific amino acid, b'c it is missing in the template structure. The Program automatically halt, if ur not removed missing aa.
Good tutorial. I have some query regarding modeling. I have some protein when I blast the sequence against PDB in ncbi they donot hit any PDB structure. So how can i choose the structure to use in modeller, or should I use ab initio methods. I am beginner. Thanks
Thank you so much for your reply. I used phyre2 and iTTaser for my protein sequences. When I used validation for my Itasser PDB the structure fail to validate. Now what should I do further very confused?
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Wow... The best modeller Tutorial on RUclips. Thank u Sir
You are most welcome
I honestly feel the background music is disturbing because we want to understand it better. But really good content, Thanks!
Sir, nice presentation, May I suggest, please can the audio be increased? so we can more listen well
Background music is very disturbing
Great video. My final year research project in bioinformatics is on endometrosis, I'm very confused about my topic. I don't know how to do research in bioinformatics. This is my first Project.
Very nice content but i feel the music background is kind of annoying, it takes away the focus. My opinion. Thank you!
Sorry about that... next video we will remove background music .. Thanks
@@jaannawaz2007 No worries, thank you for your good work!
What if my seq similarity with template is only between 30 to 37 percnt? My target showed 0 results for blastp. Any suggestion?
Please how does electro microscopy works?
Wow nice
Can you please upload a version of this video that does not have a background music? I feel that your content is very good, I just cannot focus because of the music. Please? Thanks in advance!
very informative and detailed explanations. I need one help. For hematopoietic CD34 protein, when I am searching for similar pdb structure by using of FASTA sequence, no result is coming. In your video(11:40-12:20), you have shown if we have partial structure also, we can make it by modeler. But if we do not get any similar structure what will be the alternative step? Can you please help me?
The video was very helpful. I have a doubt to ask Professor. When we look for the matching temple sequences and get 60 % identity with only a single target hit in BLASTP and it covers only the C-terminal region of the target, can the N-terminal be designed by ab inito methods like I-TASSER?
Thanks for your lovely tutorial, do you have concluding aspect on how to use this on modeller?. If not it would be nice to see the complete tutorial with modeller
Your welcome... Soon We will, if u have any doubts u can post in our facebook page
facebook.com/groups/261045198486665/
Awesome tutorial
Glad you liked it
What is the correct extension of saving the pir alignment file, " .ali " or " .ali" "? whenever I save my file with " .ali ", it gets saved as a text file. What shall I do?
in Modeller you have selected loop and multiple sequence alignment. I need suggestion for modeling of single protein for a specified sequence
Hi thank you for the lovely tutorial. I have a question, if I have an unknown sequence, can I directly use it for blastp or do I have to search for sequence homology with blast first? Thank you
Hi Sir, I would like to ask. When I edit the PDB of the template sequence, I realized there is "Connect" data after the Hetatm. Should I remove it or keep it the way it is? Thank you sir
Very nice
Very helpful tutorial, thanks.
Super.. Thank you
Thank you so much for the tutorial, but you did mention of description bord, please tell me where I could find the description bord
Best Regard
your welcome, i dont understand ur question, ... if u any errors u can post in the following facebook page..
facebook.com/groups/261045198486665/
Thanks for the useful video. Kindly can you tell how to process for a single sequence homology modeling
use similar steps ... but instead of model-multiple file u have to use model-defult.py file u can get that from this folder
C:\Program Files\Modeller9.24\examples\automodel\model-default.py
Hello and thank you for such a wonderful tutorial.
I recently started learning Homology Modeling and I would be grateful if you help me understand this:
in 17:42 you said that, in rcsb we have to check for available chains and then remove other chains in pdb file. why we have to do this? because we can define chains in modeller. we have to do such thing for all proteins when we are working on a homology modeling project?
please say something here or share a link if it is possible.
thanks again for your videos.
where to get these three script template files?
During using clustalw alignment, why few residues of my target become ---?
Sir, what is key for modeller?
PIR link is not working
Your videos are very good, they help a lot, thank you! I have a question about the alignment. Is the alignment made by the Modeller program not the best option? Do you prefer to use ClustalW? Is there a reason? Another question is about the query sequence, is there a problem removing the amino acids that are not covered by the template before running the modeling? Could this change anything in the modeling and validation process and in the results? Thank you!
1. U can use other alignment tool, u can check my video on HH Pred tool
2. if u dont remove missing aa from sequence, the program unable to find the structural conformation of the specific amino acid, b'c it is missing in the template structure. The Program automatically halt, if ur not removed missing aa.
@@jaannawaz2007 Thank you very much for replying! I'll watch the recommended video
Sir Good evening sir I'm Manohar Naik from Kadiri ,your junior in SKU I have a doubt sir
Please pause the bgm during the lecture. It is disturbing😢
PIR is not working, How to generate PIR format without expasy clustalw
Did you figure it out? I have the same issue
Thank you sir
Welcome
What next???????
Please provide the modeling tutorial.
the music in the background of the video so annoying , id appracite to you is you make it without music so we can foucs on the explination well
can you suggest any topic or some idea for homology modelling?........jisko as a m pharm project k lie kar sakte h?
Yes u can
Good tutorial. I have some query regarding modeling. I have some protein when I blast the sequence against PDB in ncbi they donot hit any PDB structure. So how can i choose the structure to use in modeller, or should I use ab initio methods. I am beginner. Thanks
Thank u .. If u don't find a homologous template, u have only option "Ab-intio" Modelling .. Soon we will release full video on Ab-intio Modeling..
Thank you so much for your reply. I used phyre2 and iTTaser for my protein sequences. When I used validation for my Itasser PDB the structure fail to validate. Now what should I do further very confused?
@@ShabirAhmad-zn1ft U mean You want to check sterochemial quality of ur I-Tasser generated PDB?
@@jaannawaz2007 yes i used the saves5 server. But failed to validate
@@jaannawaz2007 can you paste the link. bcz I am also facing the same situation. Thank you in advanced
If after Blast searching there is "No significant similarity found." I also test with swiss model, phyre2 .Then can I go for ab initio method?
Same issue . No seq similarity. What server u had used for ab initio method?
@@zainiiBee please try with I-TASSER and trRosetta server
@@sourav.chem_CU i used both .. both showing diff models. I am confused
then just compare secondary structure analysis prediction with ab-inito-modeling. and choose one.
@@sourav.chem_CU u mean Ramachandran plot?? Should i go for it ?
Would be better off without the background music
Thank you for this nice video
please send me your profile on googlescholar if you don’t mind this will be very helpful for me
Thanks alot
Ur welcome.... hr u go..... scholar.google.com/citations?user=UawBJy8AAAAJ&hl=en
I honestly feel the background music is disturbing because we want to understand it better. But really good content, Thanks!
Noted!... Next video we will remove the background Music.. Thanks