PyRx Tutorial || Multiple Ligand Docking || From Download to Result Analysis || All in One

Hi All and Welcome to OrganoMed !
This video is a complete tour to Multiple Ligand Docking using PyRx from basics to advance i.e., from software download to Result Analysis. All in one tutorial.
If this video is beneficial to you then let me know by pressing the like button and comment in the comment section. Share this video with the needy ones.
SOFTWARE USED :
PyRx : sourceforge.net/projects/pyrx/
Biovia Discovery Studio : discover.3ds.com/discovery-st...
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#moleculardocking #multipleliganddocking #pyrxdocking #docking #autodockvina #autodock #organomed

[@artisharma443]

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]

Thanks . It means a lot for me!

[@artisharma443]

@@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]

Sure. Will try to make a video soon on MD

[@yaseenjanalchemist8026]

I’m also thinking about it

[@haithamal-madhagi7769]

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.

[@decafstfu8088]

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!!!!!!!!!!

[@nathalysanchezzuleta4519]

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

[@pharmacywidmuskan]

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

[@sabrinasultana01]

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

[@himaniii5976]

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

[@cuneytdemirer269]

Awesome!

[@amey409]

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

[@yaseenjanalchemist8026]

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]

Sir which journal your articles are accepted?

[@RohitSingh-eg5ek]

Love this tutorial. Thank you so much!

[@nain9038]

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

[@anele9372]

Thank you for this video🙌

[@tanvirahmed6305]

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

[@nayanifernando6113]

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

[@snehamurugesan6109]

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

[@pasupathiable]

Extraordinary mam...

[@emediongnamkere8056]

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

[@ikarahayu3282]

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

[@agriculturelk2551]

You did a marvelous job.

[@adekashimawo53]

THANK YOU. VERY HELPFUL.

[@agriculturelk2551]

Nicely explained and really helpful. Thank you.

[@neemabisht1111]

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]

My pleasure 😊

[@mohammedsharif8985]

Thank you so much for this tutorial.

[@indukumari4407]

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

[@ayodeleoluwatosin7246]

Thank you for this awesome explanation

[@kunalsharma-db5px]

Very crisply explained & aptly presented. Thanks alot.

[@organomed]

My pleasure!

[@gurudeebanselvaraj8888]

Excellent session. Thanks for sharing...

[@organomed]

Glad to hear it!

[@josephayariga3088]

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

[@organomed]

Glad u liked it!

[@hemalathak7818]

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

[@md.mahamudulhasan6216]

This was really very helpful.
Thank you so much

[@anwarkhan4779]

Thankyou, great 👍

[@marvinprakash1612]

Very helpful.

[@anandarup-bnk]

Excellent video. Thanks a lot.

[@diptendusarkar1912]

Excellent one

[@stuti_50]

Thank you so much...Excellent Video

[@sreejithsoji2010]

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

[@parthsarthi2902]

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

[@organomed]

Glad to hear it!

[@varakalanikhilreddy6536]

Really useful vedio.
Thanks alot mam

[@shekhargaming3003]

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

[@user-re3tv1gq7t]

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

[@ericolori9858]

The video is quite informative. Thanks so much

[@omkardod9460]

Great Content

[@guruprasadanantharam4048]

Thank you so much, nice presentation

[@swetaagarwal8753]

Thanks so much, best explanation ☺☺

[@naturestruth]

Thank you very very very helpful

[@jsbiology8018]

Thank you so much!

[@AlaguPandi-zg2dw]

Thank you so much. Very nice and useful video

[@zohreghiasi5354]

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

[@logitha6129]

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

[@muhammadrafiq2260]

Very informative

[@md.mahmudulhasan5905]

THANKS .WATCHING FROM BANGLADSH

[@yadavvamsi29]

Simple clear lovely 🌹

[@kirankumarb5299]

Thanks a lot mam!!

[@ammarkareemrashidghareeb5762]

thanks a lot. so nice

[@shiprasinghal5870]

Nice explanation...thanku

[@shubhisingh7157]

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

[@ghassankhudhair1051]

very very benefits

[@dr.sciencesafaa]

Thanks ❤

[@matteo4963]

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

[@ethelchikwaro8988]

Thank you😊

[@Vishnu.vardhn6666]

Thank you so much madam

[@amandajiayeegoh9880]

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?

[@arunkumar-uo6qm]

Thank you

[@dr.thomaskurian8655]

Thank you Madam

[@Ganesh_lamichhane]

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

[@dmsek1714]

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

[@haniabaig6090]

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?

[@keerthirinil2556]

Thank you so much mam

[@vrundakumbhar5651]

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?

[@Fkkhjhkhjkjj]

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

[@aalilouyoussra3365]

thank you so much

[@grashmasadan1544]

thanks mam

[@tuanvinhle7039]

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?

[@sujithragnanasekar9091]

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

[@stutisingh9477]

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]

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

[@31stproduction90]

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?

[@pratibhagupta8816]

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.

[@cesarioajpicondori6478]

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

[@organomed]

Will try!

[@varshareddy2150]

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]

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

[@olusewa3925]

How did you overcome this, if you have.🙏

[@swatibhat8124]

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

[@zohreghiasi5354]

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

[@arjuno6992]

✨✨

[@user-qi4zt2cx2s]

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...?

[@zarlishattique4167]

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.

[@nilamsarikurniasih9323]

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?

[@harinikakumar28]

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

[@nandinibidarimath3910]

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]

Dock each protein separately...

[@dr.anujkumarborah5313]

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?

[@shereenabdalgaffar3166]

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]

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

[@jeenageorge3813]

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

[@kannanrathai2678]

Mam I have a doubt if we are taking protein for target how can we know whether the that protein is interacted with other protein..If they are interacted other protein then how we can said our interacted ligand is binding ???

[@shilpichowdhury5866]

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.

[@akshayrv130]

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

[@yadavvamsi29]

Madam my protein was not converting into macromolecule pdbqt form, it was showing some error what should I do

[@ikponwmosaobaseki3645]

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

[@khusboogupta5641]

Mam in pyrx we do minimisation but how to perform DFT if we want to do in pyrx ? Is pyrx provide this function or not??

[@malihashah3968]

Hi mam. While docking my downloaded library I get parse error on different ligands. How do I know beforehand that there's an error and how can I remove it without having my library docked all the way from the start?
The error I get is (parse error on line __ in file"..\..\Ligands\lg_name": Atom no. has not been found in this branch

[@sitiamira9807]

Hi mam, why my most affinity rmsd from vina output always 0. How can i get most correct value of rmsd which is comparable with rmsd parameter which is

[@iyarvibioinfotn6378]

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

[@organomed]

No. Not needed!