Identifying Binding Site on Protein : Tutorial
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- Опубликовано: 9 сен 2024
- In this video, I have explained my understanding on
What is a Binding Site ?
What is an Active Site ?
What is Protein-Ligand Docking ?
What is a Ligand ?
Also I have demonstrated how to vizualise the Binding site present on a protein, using PyMOL Tool (Academic Version / Educaitonal License).
This video is intended for teaching purpose.
Very helpful!, good work
Thank you
Sir could you please tell how to identify binding site a protein is not already bound with substrate or any small molecule. The crystal structure is also not available for my protein and I am using alpha fold structure. I want to perform protein-protein dockig and identify interacting amino acids among these proteins. Could you please help?
Thanks for the great tutorial. Can you make a video on how to determine the grid box dimensions? That is the xyz coordinates of the grid box!
Sooo helpful! Thank you very much for uploading !
Thank you for your Feed Back :)
sir i have one doubt. example pdb id; 1QTF structure not already bound with any small molecule, than how to find binding site of the protein?
Thanks
This is really helpful! thanks
Thank you Fauziatul.
Very nicely presented.
Thank you :)
Informative, thanks ! ❤
i want to visualize a protein protein complex docked pdb file by zooming the specific binding sites for publication.I already did the binding in pymol.But when i try to zoom the binding sites into word the figure is not very clear to see.So kindly help me on this.Thanks in advance
really great it was very helpful !!!
Sir, could you please tell me how can I find the binding sites if the ligand is not Cocrystallized?
There are some offline / online tools, that can help predict the binding pockets (Q-SiteFinder / Pocket Finder / BSpred / etc.,).
usually there are some prominent cavities on the protein surface, that can be identified as binding pocket.
Is there any way or software to analyze protein-protein docking results. Kindly guide...?
What i do in case of when ligand is not bound with protein ..so how to determine the active site in such case???
You can usually check Uniprot for the active/binding sites. It should give you a residue number which you can highlight in PyMOL.
Hello Sir, How could the ligand move without the protein moving? Thanks
So how many binding sites are there? How to get a definite number of binding site would have been helpful
Thanks. Can I share the video?
Yes, you can share this video on any social media. . Share the original video link, i.e., ruclips.net/video/49q1w0EuuhU/видео.html
Please work on your audio..it's not that clear..
Thank you for your feedback. Will work on it.
Meanwhile, plz increase your system volume to hear it clearly. Future videos, i will make more audible.