Analysing Protein-Ligand Interactions : Tutorial

This video explains the basic procedure to analyse the polar and non-polar interactions between a protein ligand complex using PyMOL software.
Protein-Ligand Interactions
Polar Interactions
Non-Polar Interactions
Color coding using PyMOL
Basic Operation of PyMOL

[@hermei8828]

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

[@preciousgarirai8406]

very helpful and well explained .. thank you so much

[@arijitdas8569]

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.

[@febiyola1655]

Thank you sir. Very good explanation

[@satishkola8643]

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

[@sciwrislifesciences2060]

Thank you for your Feed Back. .

[@sgig9608]

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

[@AsifRaza-oq4nb]

This was so smoothly explained! Thanks!

[@ashwins5180]

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!

[@sciwrislifesciences2060]

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.

[@ashwins5180]

@@sciwrislifesciences2060 yes! That must be also useful.Thank you sir and we ll wait for the next upcoming videos

[@Chiral170]

OMG thank you so much it helped a lot 👍👍

[@sciwrislifesciences2060]

Thank you Leif, Plz continue to support the channel, for the upcoming videos.

[@varakalanikhilreddy6536]

Really helpful. Thanks alot.

[@SmokeyHooder]

Very good video!

[@rekhakokkanti9508]

Thank you sir for very clear explanation. Can you show us how to remove cofactors that are co-crystallized prior to analysis?

[@sciwrislifesciences2060]

Thanks Rekha.
Yes I can make a video on that topic soon.

[@ankeetos]

Just remove the record from the pdb file

[@aprilcole2820]

@@sciwrislifesciences2060 did you ever make a video on this? I wasn't sure how to remove cofactors either.

[@sachinsahu533]

Thank you sir

[@maheenabdulrahman3367]

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?

[@shafqatphilospher5319]

Very very nice video

[@shivajidey3152]

Sir it is a wonderful explanation. Can you make a video on protein protein docking using Z dock?

[@sciwrislifesciences2060]

Thank you Shivaji.
I will work on that soon.

[@funny_product]

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

[@sciwrislifesciences2060]

Yes. Pymol can be used to measure the distance of the hydrobond aswell. I can make a video for that soon.

[@user-tc4dn9tg5y]

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]

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

[@moniruzzaman8249]

Thank you sir,

[@keyajoshi3965]

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

[@Hahahahahahahahasiu]

very good

[@haritha9370]

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.

[@nidhiaj266]

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?

[@sciwrislifesciences2060]

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.

[@dmsek1714]

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??

[@sathyacreator9612]

How to form trimeric form of protein and ligand interaction

[@wasifullahdawar6962]

Can we use this image for publication

[@rohanpawar2891]

Please make videos on MD simulations for Windows OS

[@yasa431]

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

[@rameshjethara588]

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

[@sciwrislifesciences2060]

You need to perform Protein-Ligand Docking to analyze such interactions.

[@suganyasunder6420]

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

[@ankitagoyal6926]

plzz upload how to detect active sites of protein in pymol

[@sciwrislifesciences2060]

Hi Ankita,
I have already made a video for the same. Plz check the channel for other videos.
ruclips.net/video/49q1w0EuuhU/видео.html
Identifying Binding Site on Protein : Tutorial
Hope it helps.

[@savithamurthy5718]

Sir can you speak on drug designing

[@sciwrislifesciences2060]

Hi Savitha,
Yes, I will make a video on this topic soon.

[@nilanjanajain9247]

HELLO

[@damimeyer]

VERY VERY HELPFUL !!! 1000 THANKS