Sir, is pymol shows the distance of hydrogen bonding in the interaction. Thanks to show the residue
@sciwrislifesciences20602 ай бұрын
Yes. Pymol can be used to measure the distance of the hydrobond aswell. I can make a video for that soon.
@preciousgarirai84064 ай бұрын
very helpful and well explained .. thank you so much
@hermei88285 ай бұрын
You are saving so much time with these videos! Thank you
@MashiDani10 ай бұрын
how top get file of the final result and best complex of docking to use for MD simulation
@Hahahahahahahahasiu11 ай бұрын
very good
@wasifullahdawar6962 Жыл бұрын
Can we use this image for publication
@user-tc4dn9tg5y Жыл бұрын
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
@mdzakariamorshed6778 Жыл бұрын
Can u make a video on glycosylation reaction by enzyme and substrate in presence of sugar
@SmokeyHooder Жыл бұрын
Very good video!
@adhyakk-mx8fn Жыл бұрын
The video was really thought provoking sir. Thank you
@maheenabdulrahman3367 Жыл бұрын
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?
@adityachristopher2011 Жыл бұрын
L
@NandhaKumar-dp5to Жыл бұрын
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?
@sathyacreator9612 Жыл бұрын
How to form trimeric form of protein and ligand interaction
@haritha93702 жыл бұрын
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.
@muhammadrehman41292 жыл бұрын
Is there any way or software to analyze protein-protein docking results. Kindly guide...?
@md.fahimhasan73062 жыл бұрын
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!
@damimeyer2 жыл бұрын
VERY VERY HELPFUL !!! 1000 THANKS
@keyajoshi39652 жыл бұрын
Hello. Thank you for your efforts. Will you be having any idea about analysis of polar interactions through VMD of simulation trajectories?
@AsifRaza-oq4nb2 жыл бұрын
This was so smoothly explained! Thanks!
@gauravkumar7472 жыл бұрын
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?
So how many binding sites are there? How to get a definite number of binding site would have been helpful
@yasa4312 жыл бұрын
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
@moniruzzaman82492 жыл бұрын
Thank you sir,
@shafqatphilospher53192 жыл бұрын
Very very nice video
@rohanpawar28912 жыл бұрын
Please make videos on MD simulations for Windows OS
@anjalijain56952 жыл бұрын
really great it was very helpful !!!
@josephinenimely2 жыл бұрын
Sooo helpful! Thank you very much for uploading !
@sciwrislifesciences20602 жыл бұрын
Thank you for your Feed Back :)
@satishkola86432 жыл бұрын
Remarkable informative Video sir ...thank you so much.
@sciwrislifesciences20602 жыл бұрын
Thank you for your Feed Back. .
@mkchandaliya75742 жыл бұрын
I like the last part
@arijitdas85692 жыл бұрын
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.
@suganyasunder64203 жыл бұрын
Sir please tell me how to download ligand from pubchem and convert SDF to pdb. .
@najibahsalsa3 жыл бұрын
Hello Sir, How could the ligand move without the protein moving? Thanks
@rameshjethara5883 жыл бұрын
Plz sir call me for next session I have missed this...anyway thankyou.
@rameshjethara5883 жыл бұрын
how does interaction of paracetamol and any protein can be done sir....
@sciwrislifesciences20603 жыл бұрын
You need to perform Protein-Ligand Docking to analyze such interactions.
@somaiaal-madhagy6923 жыл бұрын
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.
@varakalanikhilreddy65363 жыл бұрын
Really helpful. Thanks alot.
@dmsek17143 жыл бұрын
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??
@febiyola16553 жыл бұрын
Thank you sir. Very good explanation
@waseemahmed35843 жыл бұрын
What i do in case of when ligand is not bound with protein ..so how to determine the active site in such case???
@_lemonny3 жыл бұрын
You can usually check Uniprot for the active/binding sites. It should give you a residue number which you can highlight in PyMOL.
@sgig96083 жыл бұрын
It really helped a lot!!!! Big thanks..
@nidhiaj2663 жыл бұрын
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?
@sciwrislifesciences20603 жыл бұрын
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.
@Chiral1703 жыл бұрын
OMG thank you so much it helped a lot 👍👍
@sciwrislifesciences20603 жыл бұрын
Thank you Leif, Plz continue to support the channel, for the upcoming videos.
@johirislam81743 жыл бұрын
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
@fauziatulfitriyah55863 жыл бұрын
This is really helpful! thanks
@sciwrislifesciences20603 жыл бұрын
Thank you Fauziatul.
@ankitagoyal69263 жыл бұрын
plzz upload how to detect active sites of protein in pymol
@sciwrislifesciences20603 жыл бұрын
Hi Ankita, I have already made a video for the same. Plz check the channel for other videos. kzbin.info/www/bejne/amrUYqpmetqonrc Identifying Binding Site on Protein : Tutorial Hope it helps.
@savithamurthy57183 жыл бұрын
Sir can you speak on drug designing
@sciwrislifesciences20603 жыл бұрын
Hi Savitha, Yes, I will make a video on this topic soon.