Thank you so much, ma'am, because of this helpful video now my struggle with autodock vina etc ends and i can say people like you are boon for society

@organomed

3 жыл бұрын

Thanks . It means a lot for me!

@artisharma443

3 жыл бұрын

@@organomed it's been a month I'm struggling with autodock and different videos but your video literally solved my problem. I would love to see a video on molecular dynamics of possible

@organomed

3 жыл бұрын

Sure. Will try to make a video soon on MD

@yaseenjanalchemist8026

6 ай бұрын

I’m also thinking about it

Absolutely you are the besttttttt ever!! No more difficulties in Vina and cmd panels and other manual procedures. Thank you very very much from Syria.

Thank you so much for this. Everything is clear for me now. You explain so well.

Very thankful ma'am. I have done this. No words for thank to you. 🎉😊🙏

Thank you soooooooooo mucchhhh, srsly, i was stuck with autodock vina and also pyrx crashed several times bcz i was doing in wrong way everytime,.. u're video is soo simple yet soo effective, u've covered every issues I faced mostly.. THANK YOUUU ONCE AGAINNNN!!!!!!!!!!

Thanks a lot for this live-saving tutorial which I came across one night before my assignment's deadline 🙏 Subscribing now!!!

Thank you so much. Very well explained and easy to understand.

Love this tutorial. Thank you so much!

Thank you for this video. This video made quite easy to perform docking with multiple Ligands at one time.. Thanks for your simplified tutorial 🙏🏼

This was super duper helpful. I can't thank you enough!!!

Thanks a lot! It was probably the most useful video I found. I performed every step on my PC as the video progressed. GBU

Thank you mam! For such a clear and step by step guidance.

thank you very much for your tutorial. I had lot of question on PyRx. Now I can work on it clearly. Thank you :D

Thank you for teaching me... it's very helpful

Amazingggg vedio..👏👏after seeing this vedio my all problems related to my research work fixed Alhumdulillah .....thank you so much ❤❤

Awesome!

Thank you for this video🙌

Thanks ma'am. I am blessed with this tutorial and very nice explanation

Nicely explained and really helpful. Thank you.

Very crisply explained & aptly presented. Thanks alot.

@organomed

3 жыл бұрын

My pleasure!

Beautiful, educative, intelligent. She is awesome. God bless you. Subscribed!!!!!!

@organomed

3 жыл бұрын

Glad u liked it!

I also emailed you many times. I’m the person who have learned docking from you and now published 5 articles. Plz don’t stop making videos I was worried if something happen to you since I waited for a year only for you ❤

@rashmimahabal212

18 күн бұрын

Sir which journal your articles are accepted?

Thank you so much mam for your excellent explanation about pyrx...

You did a marvelous job.

This was really very helpful. Thank you so much

Thank you for this awesome explanation

Thank you so much for this tutorial.

THANK YOU. VERY HELPFUL.

Thank you so much. Your video is really helpful for us. 👍🙏

Thank you very much for these helpful contents,it really helped me i wish good luck for you.

Excellent session. Thanks for sharing...

@organomed

3 жыл бұрын

Glad to hear it!

Hi Mam happen to saw the video yesterday and it was very helpful.Expecting good videos like this.

Thank you so much...Excellent Video

It's very best video for understanding the Autodocking.. Thanks mam

@organomed

3 жыл бұрын

Glad to hear it!

Excellent video. Thanks a lot.

The video is quite informative. Thanks so much

thank you so much It was very, very good. Good luck.

Thank you so much. Very nice and useful video

Extraordinary mam...

Thanks so much, best explanation ☺☺

Really useful vedio. Thanks alot mam

Thankyou, great 👍

Thank you so much, nice presentation

Dear ma'am ...you explained this software in very fantastic way.....just very easygoing ....thank you so much ma'am for sharing this knowledge with us.....

@organomed

3 жыл бұрын

My pleasure 😊

THANKS .WATCHING FROM BANGLADSH

Excellent one

Very helpful.

tqq mam for ur clear explanation........

Thank you so much!

Thank you very very very helpful

Great Content

Simple clear lovely 🌹

Very informative

Nice explanation...thanku

thanks a lot. so nice

very very benefits

Thanks a lot mam!!

Thanks ❤

Thank you😊

This was really very helpful. Thank you so much. Also can you also help out with molecular dynamics simulation using GROMACS.??

thank you very much for this video... Hope you will also made some video about MOE, GOLD etc... Thank you...

Nice explanation, please do video on cytoscape ,string database and kegg pathways

Thank you so much madam

Thank you so much for these interesting and super helpful videos! I am trying to synthetize some new compounds, so I cannot download the structure of the ligands from an online database but I have to draw them by myself. I usually use Avogadro and I think I figured it out quite well, so far. The problem I am dealing with right now is that I have a carboxylate group (COO -) and I don't know how to tell the program that the oxygen atom has a negative charge on it. Should I do it with Avogadro? Should I do it with PyRx? Can the program understand it by its own? Thank you again for your videos

Thank you

Hello thank you for your video When we do multiple docking, we have to set grid box with the protein’s size???

Hi, thank you for this helpful tutorial ❤️ I have a question, using the Autodock Vina (on Autodock tools) , I had to add kollman charges to the protein during the protein preparation step. But in this tutorial, there is no such step. May I know why?

THank you so much for your clip. However, does this docking method not concern about RMSD value and only optimize the ligand by binding energy?

Thank you so much for the informative video. I have one doubt. How to get the grid box values?

thank you so much

Thank you Madam

Thank you so much mam

thank you so much ma'am, this tutorial bery helpful. I wanna ask something, how to edit my grid box in a specific active site protein receptor?

Nice explaination! how to prepare/draw ligand when we have a newly synthesized ligand?

Thank you so much for this tutorial.. Can you please tell what we can do to minimize the error of non bonded atom in Autodock?

Is the ligand energy minimization step needed if we download the protein in pdbqt format?

Its a very informative video. Thanks for it. But I wish to select some amino acid (active site) for my target protein i.e. I don't wish to do blind docking. In such case how to proceed?

thanks mam

Thank you so much..., this is going to help me in my final year project of molecular docking studies..... i am gonna use aloe ligands with spike protein for docking... also will u please help me if I need any?

It's really nice one... But as a beginner one question, are research articles accepted with good impact factor using pyrx

Thanks for this. How do we generate grid when we know the ligand binding site

✨✨

thank you very much ♥ , i support you ♥ , please can you realize a video for " how to dock an " organometallic" with protein ? " thank you again

mam, I want to know that if we download 3d structure of drug from pubchem & performed docking on drug than it's necessary to perform optimization, DFT calculation etc. for better result analysis.

Why we need to add Polar Hydrogen while creating Refine protein on Discovery Visual Tool? If I dont add it, will it be a problem while docking?

Since after minimization the name of the ligands are changed and are difficult to track , will it affect the results if we change the name of the ligands in the pyrx ligand folder...?

Thank yo very much for the tutorial. Could you make a tutorial of docking using metal-organic compunds like Auranofin?. Thanks.

@organomed

3 жыл бұрын

Will try!

Hi Why do the bonds between the ligand atoms disappear after the ligand is minimized and converted? thanks

Madam I just saw your video. It is really fecilitative to understand. But here you mentioned binding affinity as a docking score i.e. you mean both are synonymous. Is it right? If yes, then please suggest me a research publication where it is mentioned..Thanks in advance.

This video is really very helpful. Maam i have downloaded the PyRx software but not opening shows some error. How it will fix

Thanks so much for the presenter, it was really useful video. I just want to ask about use of Pyrx software with homology models as I was stuck with my protein in which heme is crucial and considered as ligand during homology modelling, Heme disappeared during conversion to pdbqt format, therefore I couldn't see protein-ligand interactions which must include heme at the the end of docking trial. I will be grateful for your kind assistance dear. Many thanks in advance..

@organomed

3 жыл бұрын

I am not very sure why is this problem arising. May be there is some mistake in protein preparation.please check carefully.

Thank you so much for these interesting and super helpful videos! subscribe Done❤

Very good explanation. Do we need to install autodock, openbabel software separately before installing Pyrx?

@organomed

3 жыл бұрын

No. Not needed!

Respected teacher, will you please tell why for all the ligands that obtained from pyrx has same 2D diagram when open in discovery studio.. for al orientation of ligand same results are there.. kindly help me to resolve the problem.

Thanks for this video! is it possible to load the drug library (PubChem/ZINC) into autodock vina or pyrx instead of downloading each ligand? Some sort of virtual screening of the 1000 compounds that were identified?

@organomed

3 жыл бұрын

You need to do it each time .you cannot directly upload all of them together..

@kebarengrakau2450

3 жыл бұрын

@@organomed Thanks for the reply

Maam what does it mean if it says atom 87 not been found while running vina wizard? What do I do?

I have a query mam After adding ligand in sdf and opening in Babel all the unsaturated bonds in ligand become saturated why?

Thanks a lot for the precise and simpler tutorial. I am wondering is there a way I can dock 2 protein with a ligand molecule.

@scienceforeveryone8827

Жыл бұрын

Dock each protein separately...

Thank you so much ma'am for the detailed explanations. You have explained it very clearly. Ma'am while making a protein macromolecule using Autodock, an error is popping up. Can you please rectify this problem?

@yadavvamsi29

2 жыл бұрын

Yes, I'm also facing the same problem, are you overcomed this problem

@olusewa3925

Жыл бұрын

How did you overcome this, if you have.🙏

Hello This video was very helpful. Can you please make a video to analyze the docking results of receptor-ligand interaction using pymol? It will be very helpful if you provide the video.

@organomed

3 жыл бұрын

Yes Sure there are lots of video tutorial to be made. I will try to make as soon as possible.