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.
Ur videos are great sir! Its very useful and the explanation was so good. Please make some videos about protocols of protein-ligand interactions and about schrodinger software. Thank you!
Thank you for your feedback Ashwin ! I currently do not have lisence for accessing Schrodinger software. How ever, I am planning to make a video on DiscoveryStudio & AutoDock softwares for protein-ligand docking. Hope those topics will be useful for 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?
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
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?
Hi Nidhi, You have to use the Original Protein.pdb file that you have given as input. If the protein structure has other heteroatoms, like Water Molecules, and othe co-crystallized molecules, this issue could occur. It can also occur, if you use the protein molecule as protein.pdbqt which is taken from the AutoDock output folder. If this is not the issue, then see if the protein structure is having any issues. Let me know if it resolved.
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.
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??
Hi Ankita, I have already made a video for the same. Plz check the channel for other videos. ua-cam.com/video/49q1w0EuuhU/v-deo.html Identifying Binding Site on Protein : Tutorial Hope it helps.
You are saving so much time with these videos! Thank you
very helpful and well explained .. thank you so much
Remarkable informative Video sir ...thank you so much.
Thank you for your Feed Back. .
This was so smoothly explained! Thanks!
Thank you sir. Very good explanation
It really helped a lot!!!! Big thanks..
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.
Ur videos are great sir! Its very useful and the explanation was so good. Please make some videos about protocols of protein-ligand interactions and about schrodinger software. Thank you!
Thank you for your feedback Ashwin !
I currently do not have lisence for accessing Schrodinger software.
How ever, I am planning to make a video on DiscoveryStudio & AutoDock softwares for protein-ligand docking.
Hope those topics will be useful for you.
@@sciwrislifesciences2060 yes! That must be also useful.Thank you sir and we ll wait for the next upcoming videos
OMG thank you so much it helped a lot 👍👍
Thank you Leif, Plz continue to support the channel, for the upcoming videos.
Really helpful. Thanks alot.
Thank you sir for very clear explanation. Can you show us how to remove cofactors that are co-crystallized prior to analysis?
Thanks Rekha.
Yes I can make a video on that topic soon.
Just remove the record from the pdb file
@@sciwrislifesciences2060 did you ever make a video on this? I wasn't sure how to remove cofactors either.
VERY VERY HELPFUL !!! 1000 THANKS
Very good video!
Sir, is pymol shows the distance of hydrogen bonding in the interaction. Thanks to show the residue
Yes. Pymol can be used to measure the distance of the hydrobond aswell. I can make a video for that soon.
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?
Very very nice video
Sir it is a wonderful explanation. Can you make a video on protein protein docking using Z dock?
Thank you Shivaji.
I will work on that soon.
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
Thank you sir
Can u make a video on glycosylation reaction by enzyme and substrate in presence of sugar
Thank you sir,
Hello. Thank you for your efforts. Will you be having any idea about analysis of polar interactions through VMD of simulation trajectories?
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?
Hi Nidhi,
You have to use the Original Protein.pdb file that you have given as input. If the protein structure has other heteroatoms, like Water Molecules, and othe co-crystallized molecules, this issue could occur.
It can also occur, if you use the protein molecule as protein.pdbqt which is taken from the AutoDock output folder. If this is not the issue, then see if the protein structure is having any issues.
Let me know if it resolved.
How to form trimeric form of protein and ligand interaction
Can we use this image for publication
very good
Please make videos on MD simulations for Windows OS
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.
how does interaction of paracetamol and any protein can be done sir....
You need to perform Protein-Ligand Docking to analyze such interactions.
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
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??
Sir please tell me how to download ligand from pubchem and convert SDF to pdb. .
plzz upload how to detect active sites of protein in pymol
Hi Ankita,
I have already made a video for the same. Plz check the channel for other videos.
ua-cam.com/video/49q1w0EuuhU/v-deo.html
Identifying Binding Site on Protein : Tutorial
Hope it helps.
Sir can you speak on drug designing
Hi Savitha,
Yes, I will make a video on this topic soon.
HELLO