Drug - Target Docking & Results Analysis Using PyRx - Vina, DS & PyMol | P1

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Animation of Docking, PyRX - Vina Tutorial, Interaction analysis and visualization using Discovery Studio and PyMol.
One thing every one must care about is ligand and target preprocessing which was not explained in detail in this video. We directly went for docking supposing that ligand and target was already preprocessed. Another video in this playlist is soon coming about how to preprocess ligands and target before docking or virtual screening.
#ligandproteindocking #PyRx #autodockvina
For part 2a (Practical tutorial) watch: • Drug - Target Docking ...
For drug discovery go to: • Drug - Target Docking ...
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[@ragheedyacob4919]

thank you so much Sir for teaching us. truly appreciate your great job.

[@ragheedyacob4919]

@@RoshanAliAcademy I am looking forward for it sir. Thank you again.

[@Cenyoh1]

Thank you so much for a detailed presentation.

[@RoshanAliAcademy]

You are so welcome dear

[@ogunoluwamayowa4749]

This video is Gold...Thanks

[@HEMAPRIYABBTYE]

Thank u for this video.....it is very helpful to us

[@kazimohammedrokanuddin2387]

thank u . nice presentation i want it.thank u so much

[@RoshanAliAcademy]

You are welcome.

[@instathambi]

thank you so much sir, i really happy after see this video, Thank you sir

[@muhammadfarhadkhan9742]

Thank You Sir Really appreciated your hard work cleared concept.. Really helpful Sir

[@RoshanAliAcademy]

I m glad you liked it and happy that my work is appreciated.

[@j.m.e.r8539]

Thank you for all work, this is really helpful !!!!

[@azkamufliha5097]

Thank you very much, sir! so clear and make me understand easily. really appreciate this :))

[@RoshanAliAcademy]

Thanx for appreciating

[@chiraggohil9145]

Osum...really helpful... can u make a video for the Drug design ?

[@stephenndombi7908]

Hi Sir, I am not able to find the active residues, could i access a link to any of your tutorials for this?

[@merve6787]

thank you for your help..

[@RoshanAliAcademy]

You are welcome dear

[@sehrishkhan2486]

thanks u so much sir, its wonderful compilation , quite helpful,appreciate ur efforts .

[@remia5]

Hi Roshan, thanks for the hard work you put into this video. I just want to know when you will be uploading the ligand and target preparations videos. Regards.

[@RajaRam-pt9xh]

thank you for the video. what to do if we want to dock with a new ligand drawn in chemdraw using this procedure?

[@Drcolisor]

Amazing job!

[@arleyr6364]

Thank you very much for the video, it is very good; more however I want to ask you a question that makes me curious: why when I do the transformation of molecules that have oxazole rings, with nitrogen atoms that do not have hydrogens, the pdbqt output file molecule presents those hydrogens where the initial molecule does not he has them?. I appreciate you help me solve this problem

[@RoshanAliAcademy]

I tried to do the same with oxazole ring containing compounds. But in my case no Hydrogen was added to the nitrogen atom on the oxazole ring.

[@elviogayozo3578]

Thanks Sir Roshan Ali for teaching us, it's a great help for everyone! I have a question, can we make protein-protein docking (e.g. protein complex predictions between two proteins or peptides) with these steps in these softwares?? Thanks a lot!

[@petelok9969]

Hello Roshnan, thank you so much for this series of videos. I'm getting so much from these. I have a question. In the general workflow would you generate a library of conformers for a given ligand using Data Warrior and then look at the orientions of each conformer in the docking study? Would that be considered good practice? Best Wishes Peter

[@RoshanAliAcademy]

No issue in following that practice. If you search KZbin, you will find a variety of different practices from experts which are all good practices

[@mni79]

good work sir

[@ManishChoudhary-hy5ey]

Roshan ..it is good effort , just reduce background sound which is distracting. Good job.

[@AyeshaKhan-rd7li]

your video is so helpful . agr ap voice ky sath krtii to or be a6y cy smj atii

[@RoshanAliAcademy]

Yes these days all my videos are with voice. These are old ones. Someone else also suggested me the same. However the video you are watching doesn't need much voice.

[@RoshanAliAcademy]

I usually avoid voice over because I want the video to be as short as possible. Voice over explanation lengthens the video.

[@ibrahimaminudanyaya7103]

Very nice job sir, I learned a lot. Sir, is there any need for homology modelling and validation of a protein with known 3D structure?

[@ibrahimaminudanyaya7103]

@@RoshanAliAcademy thank you sir for responding to my naive question. Now I have downloaded 3 proteins from PDB, which I want to use for my docking, so if I get you correct sir, it means that I have to predict a models for each of the 3 proteins by using the proteins which i have already downloaded as template right?

[@walaasalah3788]

Thank you sir roshan , now I can make docking but I don't know how to write the results and the method in my manuscript, can you help me to do that in a video

[@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

[@sirajshaikh014]

after coping protein in DS, when i open ligand window in DS and try to paste Protein (12:33 minute in video), no paste option on right click????????????????

[@RoshanAliAcademy]

No paste option or grey paste option?

[@sovendhawa9538]

Sir can we have session on how to read pyrx docked result in Chimera instead of vina as Chimera can read metal co-ordinated bond(I have heard).... Thanks in advance Sir..

[@shalushama1459]

Which protein or drug molecule we can take for a methyl coenzyme m reductase

[@RoshanAliAcademy]

In the video I just took a sample for the purpose of tutorial how to do docking. It depends on prior knowledge obtained through research articles and books, and through using tools like target prediction etc.

[@Cool_Ninga]

Please let us know why we remove water and other atoms before docking?

[@RoshanAliAcademy]

1. Water and ligands occupy space in the protein and may be inside active site which will pose hindrance during docking your ligand. The already present ligand or water will block the path to the active site for the new ligand to bind. In real life the new ligand can easily replace water in the active site and can enter into the active site, but in docking which is not a real life simulation, your new ligand cannot push or do not know how to push them aside to enter into the active site. 2. If water molecules are present then it will make your docking a lot longer, Therefore to reduce the time of docking we remove them. 3. Water molecules do not usually take part in binding the ligand to the active site. 3. Those water molecules which are involved in the interaction with your ligand, they are not removed.

[@maryamzaman671]

the video is very helpful.i perform the docking of my protein by watching the video.but when i proceeding the last step after define receptors when i click on show 2d images it shows error plz help me to sort it out i will be grateful

[@ERMIE2024]

Is PyMol RX a free tool , or is it commercial software? How to obtain?

[@RoshanAliAcademy]

Both PyMol and pyrx have free as well as commercial versions. U can use free versions

[@VishalMevada102]

Can we analyze the multiple ligands at once and export its binding interaction to excel of other software?

[@VishalMevada102]

@@RoshanAliAcademy Share the link for that video. Appreciate your time and response.

[@mousumibhattacharjee7570]

How to find the active amino acid residues?? Please illustrate

[@Cool_Ninga]

2ndly, how to interpret the docking of ligand and protein for write up. I mean to say how to narrate the whole procedure? Please guide...

[@RoshanAliAcademy]

For this I think it would be better to find a docking related article on Google Scholar. From there you can get the idea, how author write up about ligand-target interaction. They usually write up about the bonds between the ligand and the protein. And also the importance and role of those interactions in blocking the protein, or curing the disease, or inhibiting the viral protein from interring the host cell..

[@ajamerlan]

Do the output files get automatically saved to the folder after the run is completed? Can I close the program after the run?

[@RoshanAliAcademy]

You mean PyRx results?

[@ajamerlan]

@@RoshanAliAcademy yes, I mean PyRx. Once the PyRx run is over, can I close it and the result gets saved automatically into the specified folder?

[@arifpasha83]

hi sir will u plz tell me defining ligand iam not getting only receptor is getting selected plz do the needful

[@Faizanmalik-rt4ft]

Select hetatm and not orientation

[@venckaazzahra5885]

I already click the ligand and then define ligand but its still undefined, and the show 2d diagram option cannot be clicked. How can i fix this?

[@RoshanAliAcademy]

Try the other ways. For example: dont click on ligand and then try to define ligand. sometimes this work, or just click the main protein molecule and define the ligand without clicking on it. Tell me if it works

[@venckaazzahra5885]

@@RoshanAliAcademy it didnt work, and it keep saying 'no ligand molecules were found'

[@RoshanAliAcademy]

@@venckaazzahra5885 can you tell me your protein PDB ID so that I can try it by myself and see if it works

[@venckaazzahra5885]

@@RoshanAliAcademy my protein pdb id is 3HF1 (crystal structure of p53r2) but the ligand is not from zinc15 or pubchem, because it's a new compound and still not available there, so i make the ligand from chemdraw software. Is it because of that?

[@RoshanAliAcademy]

@@venckaazzahra5885 Ummmm, that could be the reason.

[@arshyamktk6322]

What is the use of docking or future of docking

[@arshyamktk6322]

How could i download research article without purchasing? Is there any other method to download article?

[@andrelucena3232]

@@arshyamktk6322 Try sci-hub.tw you'll need the DOI of the article, which is provided by repositories (e.g NCBI)

[@rashamoustafa427]

🌺🌺🌺🌺🙏🙏🙏🙏

[@RoshanAliAcademy]

Thank you dear

[@haechanie6859]

Start in 4:23

[@RoshanAliAcademy]

Appreciated

[@AyeshaKhan-rd7li]

where are you from

[@RoshanAliAcademy]

Pakistan

[@AyeshaKhan-rd7li]

which city @@RoshanAliAcademy

[@AyeshaKhan-rd7li]

can you help me in my resurch . on molecular docking

[@RoshanAliAcademy]

Parachinar

[@RoshanAliAcademy]

Yes why not

[@nitishchauhan3406]

Hello, I am using the latest PyRx free version software. I follow all the necessary steps required for docking that was mentioned in PyRx tutorial videos. But, here the problem comes when I visualized docking results in PyMol/ DS visualizer as the interacting partners and H-bonded amino acids were different from the interacting amino acid which was already published in peer journals. I repeated the same for many protein n ligands exactly the same which were given in published papers, but every time result is the same. I pushed n tried very hard but nothing is working, so please help me. You can hand on this- PDB ID-6LU7, ligand- Lopinavior, if the docking with PyRx is fine, then the docking result must show the same interaction as in the picture, or u can see in the article. doi.org/10.20944/pr... Thank u in Avance

[@sehrishkhan2486]

thanks u so much sir, its wonderful compilation , quite helpful,appreciate ur efforts .