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

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

[@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. 🎉😊🙏

[@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?

[@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 😊

[@adiohworukevwe1746]

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

[@rudzanimatodzi9803]

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

[@parthsarthi2902]

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

[@organomed]

Glad to hear it!

[@tanvirahmed6305]

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

[@sabrinasultana01]

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

[@josephayariga3088]

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

[@organomed]

Glad u liked it!

[@kunalsharma-db5px]

Very crisply explained & aptly presented. Thanks alot.

[@organomed]

My pleasure!

[@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 🙏🏼

[@snehamurugesan6109]

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

[@nathalysanchezzuleta4519]

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

[@ikarahayu3282]

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

[@sreejithsoji2010]

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

[@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

[@pasupathiable]

Extraordinary mam...

[@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

[@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.

[@anele9372]

Thank you for this video🙌

[@emediongnamkere8056]

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

[@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

[@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.🙏

[@dr.sciencesafaa]

Thanks ❤

[@adekashimawo53]

THANK YOU. VERY HELPFUL.

[@jeenageorge3813]

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

[@gurudeebanselvaraj8888]

Excellent session. Thanks for sharing...

[@organomed]

Glad to hear it!

[@shekhargaming3003]

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

[@Vishnu.vardhn6666]

Thank you so much madam

[@anusuyanagaraj7845]

thank you

[@Ganesh_lamichhane]

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

[@shreyatubee]

many many thanks

[@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?

[@ayodeleoluwatosin7246]

Thank you for this awesome explanation

[@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?

[@agriculturelk2551]

You did a marvelous job.

[@swetaagarwal8753]

Thanks so much, best explanation ☺☺

[@ericolori9858]

The video is quite informative. Thanks so much

[@RohitSingh-eg5ek]

Love this tutorial. Thank you so much!

[@shubhisingh7157]

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

[@dmsek1714]

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

[@md.mahamudulhasan6216]

This was really very helpful. Thank you so much

[@stuti_50]

Thank you so much...Excellent Video

[@logitha6129]

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

[@AlaguPandi-zg2dw]

Thank you so much. Very nice and useful video

[@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?

[@agriculturelk2551]

Nicely explained and really helpful. Thank you.

[@mohammedsharif8985]

Thank you so much for this tutorial.

[@anandarup-bnk]

Excellent video. Thanks a lot.

[@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.

[@ethelchikwaro8988]

Thank you😊

[@zohreghiasi5354]

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

[@dr.thomaskurian8655]

Thank you Madam

[@guruprasadanantharam4048]

Thank you so much, nice presentation

[@varakalanikhilreddy6536]

Really useful vedio. Thanks alot mam

[@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.

[@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?

[@naturestruth]

Thank you very very very helpful

[@yadavvamsi29]

Simple clear lovely 🌹

[@cuneytdemirer269]

Awesome!

[@indukumari3230]

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

[@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

[@shiprasinghal5870]

Nice explanation...thanku

[@swatibhat8124]

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

[@indranisarkar3901]

Madam please give a presentation of site specific docking by pyrx. Thank you

[@organomed]

Sure. I will try to make it soon.

[@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?

[@anwarkhan4779]

Thankyou, great 👍

[@kirankumarb5299]

Thanks a lot mam!!

[@shamsnoorbakhsh2126]

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

[@indranisarkar3901]

after docking molecular dynamics is needed .Pl give a demo also on minimization and dynamics and analysis of result

[@organomed]

Yes sure!

[@jsbiology8018]

Thank you so much!

[@ammarkareemrashidghareeb5762]

thanks a lot. so nice

[@indranisarkar3901]

the video was very helpful. Can site specific docking be done with pyrx? Also explanation of docking results more elaborately will help

[@organomed]

Yes you can perform site specific docking in pyrx.

[@dr.indranisarkar4671]

@@organomed please post site specific docking with pyrx

[@keerthirinil2556]

Thank you so much mam

[@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

[@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!

[@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.

[@SAMSONPRINCEH]

Is pyrx used to analyse protein protein interaction

[@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.

[@muhammadrafiq2260]

Very informative

[@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

[@markundaberbere2425]

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

[@ReadwithFacts]

Hello mam..... Why do we delete Hetatm from PDB file before docking?

[@kritikamehta4735]

Hi I am facing problem while running Pyrx software.After resizing the grid box when i select forward it shows;stderr :an unknown error occurred. version 0.8 operating system : window 10 ,hp i3 10 gen

[@organomed]

Did you prepared your protein properly or not? May be that's the reason it's showing error.

[@anubhavchauhan7371]

@Kritika Mehta did you problem got sloved?

[@ghassankhudhair1051]

very very benefits

[@abdeldjebarhasnia1788]

Hi, I am trying to dock a compound which contains Copper. I got this error while performing autogrid. Can you please help me with this error : \autogrid4.exe: ERROR: unknown ligand atom type Cu add parameters for it to the parameter library first!

[@organomed]

autodock.scripps.edu/faqs-help/faq/how-do-i-add-new-atom-types-to-autodock-4 Check it out!

[@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?

[@Fkkhjhkhjkjj]

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

[@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...

[@zahraaammer8700]

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

[@iyarvibioinfotn6378]

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

[@organomed]

No. Not needed!

[@santhiamala797]

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