Computational Vaccine Designing | Protein-Protein Docking | ClusPro | PDBsum | Hand-on Training
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- Опубликовано: 11 сен 2024
- This video will help you to perform docking of your two desired proteins and will also assist you to check the type of interactions between your docked proteins. Different tools are introduced plus the results are explained in detail.
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Assalamualaikum Sir,
Two questions:
1. sometimes (in research articles) the vaccine construct is docked with TLR and sometimes it is docked with MHC molecule. How to know that which is more preferable?
2. If I have to dock HLA allele, how to know that which allele should I dock with Epitope or Vaccine?
Thanks
Walaikom assalam...I am glad that you are watching my tutorials with full interest...
You are right, most of the articles chooses different immune receptors. Its a common understanding that the mentioned immune receptors in the video are the most common and have huge roles in immune cells activation and functioning. I recommend to use all the mentioned ones in order to check the efficiency of your vaccine. There are also other immune receptors that are used by the scientists to be docked with the vaccine as well...Thanks
Sorry for the next question, I didnot get the logic of that question...thanks...
Good luck...
Thanks for the video! When I download my files from ClusPro onto PDBSum it says wrong file format! Any suggestions?
View the docked complexes in notepad++ before processing via PDBsum... clustro mostly merge the protein subunits into other subunits...you have to rename the chains as they were before...I am sharing a link of my video that litrally explain the issue in other context but u can get the point from there...Thanks
ruclips.net/video/VQz7W9Glr-U/видео.htmlsi=YYOERDV0mTvvVIV_
May I ask why you said vaccine goes on to the receptor side and other proteins like TLRs or any othe rmolecule on ligand side?
it was only to differentiate between the two entities..thats all you can use the words interchangebaly in this case...but if u r dealing with ligands like drug compounds or other non-proteinous entities, then u will called it ligand...thanks
Thank you @@scienceforeveryone8827
Why dont you make video on Md simulation as well it will b really appreciated.
well sorry for that but i am not having resources for it...you can use online tools as iMOD and SiBioLead for your MD simulations...there are many tutorials about it...good luck for your research...
@@scienceforeveryone8827 ok thanks cn I get ur email?
nadeemkhanf577977@gmail.com
Hello sir, hope you are doing well, I am talking from Bangladesh. I have an error when I am trying to visualize the docking complex using the webserver (PDBsum) as you mentioned here. I have done all the steps in my work but here in PDBsum there is a kind of message (Uploaded file contains non-unique chain identifiers. Please check that your PDB file conforms to correct PDB conventions) please assist me in solving the problem
hi, i am glad that my vidoes are helping out...before docking throughly check out your protein and make sure that it should not have any ligands attach. Secondly, after docking, there is chance that the chain of one protein might have merged into the other protein ( this usually happens in protein-protein docking. Before viewing in PDBsum, open your complexes in notepad ++ tool. Than throughly check the chain id means e.g your vaccine have a single chain named A and your other protein might have chain B, C and D etc. Than there is a chance that chain B amino acids might be replaced with chain C id etc etc. Go through each chain id and rename it if you see any merging...i am sharing you a tutorial video form my channel that have merely explain this concept, you might get the idea form there...Thanks
ruclips.net/video/VQz7W9Glr-U/видео.htmlsi=Q0KeHsvtuKz4YiMI
Thank you so much for your kind reply@@scienceforeveryone8827
thank you. It worked@@scienceforeveryone8827
if cluspro is not working insted of this which tool can be used
Patchdock...thanks
Can we use Hdock web server to dock vaccine candidate against TLR3 human receptors?
I get -346 docking score in Hdock
Target > NS5 Rdrp of zika virus
Is it good??? For Ms project
95.2% Ramachandran favr
0.0%
yes, the docking score is in acceptable range, also check the interactions via PDBsum tool as shown in this video..This will strenghten your objective...Ramachandaran stats are also good enough...Thanks
@@scienceforeveryone8827 thnk u
sir why we do intraction analysis
In order to check the type of interactions present between our designed vaccine and the immune receptors plus also want to see the amino acids involved in the interactions from both sides...Have discussed this in detail in the tutorial...Thanks
sir why we not take mhc 1 molecule
Because its present over the immune cells and also on normal cells and is highly specific to immune activations
How about MD simulation bro?
use Imod or SiBioLead servers for it
Assalam o Alaikum
Sir I am unable to creat an account. Can you forward me your email and password to me or do my docking yourself. I can provide you the files.
walaikom assalam...well if you open the main page of the cluspro, there is a heading "use the server without the benefits of your own account". click on it and you can perform the docking without any id...thanks...even i had perform it via this method...thanks