SciWris Life Sciences

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@muntasiralam9127 15 күн бұрын

Sir,thank you for your video. I have some ligand which have only 2D structure but no 3D. so, can i do docking with the 2D structure?

@hujjatullah97 Ай бұрын

Very helpful sir

@snehapradeep5150 3 ай бұрын

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

@juanjesuslopezvillafuerte6338 5 ай бұрын

Very helpful!, good work

@cemilemol6729 5 ай бұрын

Thank you

@funny_product 8 ай бұрын

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

@sciwrislifesciences2060 6 ай бұрын

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

@preciousgarirai8406 9 ай бұрын

very helpful and well explained .. thank you so much

@hermei8828 10 ай бұрын

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

@MashiDani Жыл бұрын

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

@IloveLeeDaHye Жыл бұрын

very good

@wasifullahdawar6962 Жыл бұрын

Can we use this image for publication

@SudhaMerla 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 2 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 2 жыл бұрын

@NandhaKumar-dp5to 2 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 2 жыл бұрын

How to form trimeric form of protein and ligand interaction

@haritha9370 2 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.

@muhammadrehman4129 2 жыл бұрын

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

@md.fahimhasan7306 2 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!

@damimeyer 2 жыл бұрын

VERY VERY HELPFUL !!! 1000 THANKS

@keyajoshi3965 2 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-oq4nb 2 жыл бұрын

This was so smoothly explained! Thanks!

@gauravkumar747 2 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?

@sakshivarshney3563 2 жыл бұрын

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

@victuskordorwu867 2 жыл бұрын

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

@yasa431 2 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

@moniruzzaman8249 2 жыл бұрын

Thank you sir,

@shafqatphilospher5319 3 жыл бұрын

Very very nice video

@rohanpawar2891 3 жыл бұрын

Please make videos on MD simulations for Windows OS

@anjalijain5695 3 жыл бұрын

really great it was very helpful !!!

@josephinenimely 3 жыл бұрын

Sooo helpful! Thank you very much for uploading !

@sciwrislifesciences2060 3 жыл бұрын

Thank you for your Feed Back :)

@satishkola8643 3 жыл бұрын

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

@sciwrislifesciences2060 3 жыл бұрын

Thank you for your Feed Back. .

@mkchandaliya7574 3 жыл бұрын

I like the last part

@arijitdas8569 3 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.

@suganyasunder6420 3 жыл бұрын

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

@najibahsalsa 3 жыл бұрын

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

@rameshjethara588 3 жыл бұрын

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

@rameshjethara588 3 жыл бұрын

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

@sciwrislifesciences2060 3 жыл бұрын

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

@somaiaal-madhagy692 3 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.

@varakalanikhilreddy6536 3 жыл бұрын

Really helpful. Thanks alot.

@dmsek1714 3 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??

@febiyola1655 3 жыл бұрын

Thank you sir. Very good explanation

@waseemahmed3584 3 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???

@_lemonny 3 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.

@sgig9608 3 жыл бұрын

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

@nidhiaj266 4 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?

@sciwrislifesciences2060 4 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.

@Chiral170 4 жыл бұрын

OMG thank you so much it helped a lot 👍👍

@sciwrislifesciences2060 4 жыл бұрын

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

@johirislam8174 4 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

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