Identifying Binding Site on Protein : Tutorial

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.

[@juanjesuslopezvillafuerte6338]

Very helpful!, good work

[@cemilemol6729]

Thank you

[@gauravkumar747]

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?

[@md.fahimhasan7306]

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!

[@josephinenimely]

Sooo helpful! Thank you very much for uploading !

[@sciwrislifesciences2060]

Thank you for your Feed Back :)

[@NandhaKumar-dp5to]

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?

[@sachinsahu533]

Thanks

[@fauziatulfitriyah5586]

This is really helpful! thanks

[@sciwrislifesciences2060]

Thank you Fauziatul.

[@amreenkhan5076]

Very nicely presented.

[@sciwrislifesciences2060]

Thank you :)

[@shabarigirish5058]

Informative, thanks ! ❤

[@johirislam8174]

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

[@anjalijain5695]

really great it was very helpful !!!

[@suprajatap9945]

Sir, could you please tell me how can I find the binding sites if the ligand is not Cocrystallized?

[@sciwrislifesciences2060]

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.

[@muhammadrehman4129]

Is there any way or software to analyze protein-protein docking results. Kindly guide...?

[@waseemahmed3584]

What i do in case of when ligand is not bound with protein ..so how to determine the active site in such case???

[@_lemonny]

You can usually check Uniprot for the active/binding sites. It should give you a residue number which you can highlight in PyMOL.

[@najibahsalsa]

Hello Sir, How could the ligand move without the protein moving? Thanks

[@victuskordorwu867]

So how many binding sites are there? How to get a definite number of binding site would have been helpful

[@nurulhafizan4984]

Thanks. Can I share the video?

[@sciwrislifesciences2060]

Yes, you can share this video on any social media. . Share the original video link, i.e., ruclips.net/video/49q1w0EuuhU/видео.html

[@saranyadey9946]

Please work on your audio..it's not that clear..

[@sciwrislifesciences2060]

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.