Filling Missing Residue in PDB Structure Using Modeller | Homology Modelling | Bioinformatics
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- เผยแพร่เมื่อ 11 ก.ย. 2024
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In this video, we will teach you how you can fill the gaps in protein 3D structures using Modeller. Please remember that you can not use the structure with missing residues for docking, and molecular docking simulations.
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can you please put applied scripts for us here or tell us where we can get these essential scripts to repair the sequence?
First if you make a tutorial you should keep your scripts accessible and don't hide them. Second, all of these steps can be done automatically in chimera.
Hi sir Mohammed, that's true and one main problem with is that after inspection of the model structure you notice a change in the amino acid residues like they have been replaced by other amino acides.
I agree and apologise for not providing scripts
Hi! Do you have a tutorial for doing this automatically in chimera? Thanks!
@@carolinesargent2998 I will post this as soon as I have time
Excellent explanation and very helpful because homology modeling and filling missing residue in pdb has some differences. It will be helpful and can devoid confusions if you upload related pre-requiste files like previous tutorial please..
You are most welcome. sure we will
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Such a great teacher I have ever seen in my life...thank u soo much sir for teaching us in this way, such an outstanding way of teaching. May Allah always bless u 💟 appreciated 👏👏
Many thanks Shanza
from where i can the script files?
These scripts are available at Modeller website. We have customized the scripts and they are available in our course at Udemy Bioinformatics: Learn Docking and MD Simulation from Scratch.
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what to do if plenty of molecules is missing in the middile of the sequence it self ?
you can fix them all easily using described methodology in video
My protein has missing atoms in some of the residues instead of whole residues can this fix that ?
Am wondering , cant the descovery stodio fix it all with clean geometry option ?!
To some extent yes, but Modeller is considered gold standard so far.
hello sir, I have a query:- I have a protein PDB ID 4HJO. in it the residues are missing in the begining, in the midlle region and at the end how to make changes in the script 3 so as to execute it w ithout any error, please help as I am stuck with it ? thank you
Dear Altaf Ahmad Shah, many thanks for watching our videos. Please do not worry for the residues that are missing at the start and end. You just need to focus on the middle one. Hope it will help you out
Dear Altaf, Im trying to do this tutorial but I cant find the cripts and the comment section is not helping. Could you please share the script files or tell me where can I get them? Is it on the Udemy course?
@@dennisag4936 drop your mail here i will send the link. else you can find the scripts given in Modeller tutorial link site
Thanks for uploading this video. Can you please share python scripts 1, 2 and 3 used in this video?
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salilab.org/modeller/wiki/Missing_residues
Simple and excellent
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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.
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Do we have to use these same scripts for all proteins??
Yes
Nice explanation, how can we fill missing residues of a protein containing two or more chains ?
salilab.org/modeller/wiki/Missing_residues
Yes you can
Can you please share python scripts 1, 2 and 3 used in this video?
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where to get these 3 script template files?
Please visit the Modeller website. You can find all scripts there.
can you provide the direct links@@bioinfoxpert
need the scripts
Upload all the script files which is used in this video fast
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(www.udemy.com/course/bioinformatics_advance/?referralCode=E0E70A2ABEDEEB5F3D68)Click Below To Get Two Best Seller Courses To Learn Bioinformatics From Zero
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