Homology Modeling for Beginners | COVID19 NP Protein Modeling Modeller Tutorial | Bioinformatics
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Published 2020-06-18
In this video (Session -1), we covered a basic introduction to homology modelling and hands-on pipeline on homology modelling using Modeller tool.
Modeller Software: salilab.org/modeller/
Modeller Tutorial: salilab.org/modeller/tutorial/basic.html
Homology Modelling Softwares and Webserver: en.wikipedia.org/wiki/List_of_protein_structure_pr…
PIR file server: embnet.vital-it.ch/software/ClustalW.html
Verify 3D: servicesn.mbi.ucla.edu/Verify3D/
Homology Modelling Basics:
journals.plos.org/ploscompbiol/article?id=10.1371/…
All Comments (21)
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Wow... The best modeller Tutorial on Youtube. Thank u Sir
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I honestly feel the background music is disturbing because we want to understand it better. But really good content, Thanks!
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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
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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?
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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.
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Sir, nice presentation, May I suggest, please can the audio be increased? so we can more listen well
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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
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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?
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in Modeller you have selected loop and multiple sequence alignment. I need suggestion for modeling of single protein for a specified sequence
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Very helpful tutorial, thanks.
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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.
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What if my seq similarity with template is only between 30 to 37 percnt? My target showed 0 results for blastp. Any suggestion?
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Super.. Thank you
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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?
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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
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During using clustalw alignment, why few residues of my target become ———?
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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!
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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!
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Please how does electro microscopy works?
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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
