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How to visualise the surface properties electrostatics and map the interaction of a pocket

Very helpful!, good work

Thank you

Sir, is pymol shows the distance of hydrogen bonding in the interaction. Thanks to show the residue

very helpful and well explained .. thank you so much

You are saving so much time with these videos! Thank you

how top get file of the final result and best complex of docking to use for MD simulation

very good

Can we use this image for publication

What are Gasteiger and Kollman charges? Where exactly are these charges being added in the protein? How can I determine the location of these charges in the protein

Can u make a video on glycosylation reaction by enzyme and substrate in presence of sugar

Very good video!

The video was really thought provoking sir. Thank you

Sir please upload one video for docking for knowing the blinding interaction between protein protein (gene-gene) interaction 8n autodock ..is it possible in it?

L

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?

How to form trimeric form of protein and ligand interaction

When we require to find the binding site residue, do we have to consider only the residues involved in polar interaction or both polar and non-polar? Pls do reply sir.

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

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!

VERY VERY HELPFUL !!! 1000 THANKS

Hello. Thank you for your efforts. Will you be having any idea about analysis of polar interactions through VMD of simulation trajectories?

This was so smoothly explained! Thanks!

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?

Registration link: docs.google.com/forms/d/e/1FAIpQLScwZFVqxqbnfYOHKFvjgjbJ0yCPDOBmBq5sK_cRni_-yJV4CQ/viewform

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

Hello sir I would really really appreciate if you can do a video on changing amino acids from l to d amino acids in pymol

Thank you sir,

Very very nice video

Please make videos on MD simulations for Windows OS

really great it was very helpful !!!

Sooo helpful! Thank you very much for uploading !

Remarkable informative Video sir ...thank you so much.

I like the last part

I appreciate your informative and simple guide. I request your instructions via a tutorial video on how to dock heavy metal ligands (like Palladium oxide or Silver) to a protein using Autodock 4.2.

Sir please tell me how to download ligand from pubchem and convert SDF to pdb. .

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

Plz sir call me for next session I have missed this...anyway thankyou.

how does interaction of paracetamol and any protein can be done sir....

please sir explain how can I set the grid box dimensions if the ligand I am trying to test (not the original ligand crystalized with the protein) lays far away from the protein (when I input the ligand to AutoDock 4)?? When I tried to cover both ligand and protein inside the grid, the grid box was very big which causes an error message to pop up may times.

Really helpful. Thanks alot.

hello, if i have to compare the functiom of inhibition of 2target cell from inhibitor, what i have to do?? i already get each protein~inhibitor complex, how can i compare these 2 complex??

Thank you sir. Very good explanation

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

It really helped a lot!!!! Big thanks..

Thank you sir. it is very much helpful. Sir, if we are taking protein and ligand separately( protein.pdb and output.pdbqt), and trying to find [action-preset-ligands] , i am getting the polar bond for the whole protein, how do i do to get the polar and non-polar residues only nearby the ligand?

OMG thank you so much it helped a lot 👍👍

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

This is really helpful! thanks

plzz upload how to detect active sites of protein in pymol