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

[@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

[@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?

[@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!!!!!!!!!!

[@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.

[@nain9038]

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

[@pharmacywidmuskan]

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

[@rudzanimatodzi9803]

I am here 2024,this is great. Please continue posting 😊

[@adiohworukevwe1746]

This video was very helpful, thank you. You're a lifesaver.

[@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 😊

[@sabrinasultana01]

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

[@parthsarthi2902]

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

[@organomed]

Glad to hear it!

[@kakarlapakeeraiah2580]

Thank you very much for your explanation It's very interesting and useful who are in early learning stage

[@kunalsharma-db5px]

Very crisply explained & aptly presented. Thanks alot.

[@organomed]

My pleasure!

[@josephayariga3088]

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

[@organomed]

Glad u liked it!

[@emediongnamkere8056]

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

[@gurudeebanselvaraj8888]

Excellent session. Thanks for sharing...

[@organomed]

Glad to hear it!

[@snehamurugesan6109]

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

[@tanvirahmed6305]

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

[@sreejithsoji2010]

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

[@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 🙏🏼

[@ikarahayu3282]

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

[@indukumari4407]

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

[@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

[@nathalysanchezzuleta4519]

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

[@pasupathiable]

Extraordinary mam...

[@ranamukherjee3741]

Thank you so much. Very good explain 🎉

[@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

[@ayodeleoluwatosin7246]

Thank you for this awesome explanation

[@agriculturelk2551]

You did a marvelous job.

[@anele9372]

Thank you for this video🙌

[@varakalanikhilreddy6536]

Really useful vedio. Thanks alot mam

[@swetaagarwal8753]

Thanks so much, best explanation ☺☺

[@ericolori9858]

The video is quite informative. Thanks so much

[@rashmimahabal212]

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

[@md.mahmudulhasan5905]

THANKS .WATCHING FROM BANGLADSH

[@stuti_50]

Thank you so much...Excellent Video

[@hemalathak7818]

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

[@AMIRPASHAIE-h7v]

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

[@md.mahamudulhasan6216]

This was really very helpful. Thank you so much

[@anandarup-bnk]

Excellent video. Thanks a lot.

[@zohreghiasi5354]

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

[@shekhargaming3003]

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

[@adekashimawo53]

THANK YOU. VERY HELPFUL.

[@omkardod9460]

Great Content

[@RohitSingh-eg5ek]

Love this tutorial. Thank you so much!

[@agriculturelk2551]

Nicely explained and really helpful. Thank you.

[@yadavvamsi29]

Simple clear lovely 🌹

[@uos.chemist1437]

Dear great and innovative way of transferring the knowledge among the beginners. Kind share the complete setup of pyrx in ziped or google drive because i am unable to download the pyrx. Please share the setup. Thanks

[@diptendusarkar1912]

Excellent one

[@AlaguPandi-zg2dw]

Thank you so much. Very nice and useful video

[@guruprasadanantharam4048]

Thank you so much, nice presentation

[@mohammedsharif8985]

Thank you so much for this tutorial.

[@dr.sciencesafaa]

Thanks ❤

[@dmsek1714]

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

[@shiprasinghal5870]

Nice explanation...thanku

[@muhammadrafiq2260]

Very informative

[@logitha6129]

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

[@CHEBROUKFarid]

excellent, Thks

[@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.🙏

[@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?

[@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?

[@marvinprakash1612]

Very helpful.

[@Ganesh_lamichhane]

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

[@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.

[@anwarkhan4779]

Thankyou, great 👍

[@jeenageorge3813]

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

[@indukumari3230]

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

[@thebiobuddy9595]

U are just awesome

[@talitafreitas4341]

Hello. Some questions: how will I reproduce a redocking protocol in Pyrx? And how did you know that model 1 among the 9 was of interest to you? Thank you for your attention and congratulations on the video.

[@organomed]

The protocol is same as that in AutoDock Vina. Out of all models check the RMSD value. The lower RMSD value will have greater accuracy.

[@talitafreitas4341]

@@organomed So should I consider the values ​​where both RMSD and Mode are zero? And those who have RMSD and Mode different from zero but with the same binding affinity as RMSD and Mode equal to zero?

[@organomed]

@@talitafreitas4341 The conformation having highest binding affinity is compared to itself hence it's RMSD is 0. After that subsequent modes are compared to the first one so they have deviation in RMSD.

[@cuneytdemirer269]

Awesome!

[@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?

[@nusratafrin898]

Do we need to make a ligand library prior to docking?

[@naturestruth]

Thank you very very very helpful

[@akshayrv130]

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

[@shamsnoorbakhsh2126]

Thanks so much . How can i enter my center for grid box?

[@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?

[@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?

[@kebarengrakau2450]

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]

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

[@kebarengrakau2450]

@@organomed Thanks for the reply

[@harinikakumar28]

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

[@shubhisingh7157]

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

[@SAMSONPRINCEH]

Is pyrx used to analyse protein protein interaction

[@yadavvamsi29]

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

[@SudhaMerla]

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

[@ethelchikwaro8988]

Thank you😊

[@ummeaiman9697]

Mam can we do multiple proteins ligands docking as well with this ..plz answer

[@iyarvibioinfotn6378]

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

[@organomed]

No. Not needed!

[@Vishnu.vardhn6666]

Thank you so much madam

[@kirankumarb5299]

Thanks a lot mam!!

[@zahraaammer8700]

If i have a peptide ligand with 20 amino acids would it work??

[@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 ???

[@sonuverma1901]

I want to know is it possible to perform docking for 200 ligands? Kindly reply.

[@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.

[@parthsharma6079]

hii maam after installation autodock and mgltools it is not opend in my ryzen3 based laptop please provide some suggestions why it is looking so

[@shreyatubee]

many many thanks

[@harithak5102]

Hello mam, how can we carry out docking of a new molecule whose structure is not available in pubchem

[@Fkkhjhkhjkjj]

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

[@ammarkareemrashidghareeb5762]

thanks a lot. so nice

[@santhiamala797]

Mam What we should do if we dint find ligand from Zinc database and pub chem.Please clarify this doubt mam

[@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?

[@AreebaKhan-wi8vc]

I've been following the same steps. However, after docking, my results are coming in positive... which is wrong .. what should i do ?