Protein-ligand virtual docking using PyRx | Computational biology | Bioinformatics | Akash Mitra

🕸Website - akashmitraa.github.io/persona...
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🎵Study with me Playlist - open.spotify.com/playlist/6oN... This video demonstrates a detailed procedure of the virtual docking using PyRx and how me can visualize the same in PyMOL. This is one of the fundamental technique used in drug designing.
Download links
PyRx : sourceforge.net/projects/pyrx/
Open Babel : sourceforge.net/projects/open...
PyMOL : pymol.org/2/
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🎵Study with me Playlist - open.spotify.com/playlist/6oN...
Who am I -
I'm Akash, a Microbiologist 🔬 and a freelance Biology Teacher. I like making videos and spending time making my study sessions pleasurable although that sounds weird😅. I also help high school kids with their biology lessons.
If you would like to talk about the video or anything in general, just drop a word on Facebook or if you have a really long question then shoot me an email at [e-mail]. I would surely respond 😃

[@adittyakhan1791]

You are a lifesaver bro. Thanks

[@micberpra]

Excellent explanation.

[@SarkisDallakian]

Great video! Thank you.

[@SarkisDallakian]

@@akashmitrabiology Sure, I've added this to PyRx Blog - pyrx.sourceforge.io/blog. A couple of notes worth sharing: PyRx includes OpenBable, so probably could have done sdf to pdbqt conversion in PyRx. Also, Vina is not written in Python, but C/C++. It runs super fast and it can utilize multiple CPU cores.

[@laymanreacts4130]

It was So Cool bro!!

[@bdvetscorner376]

Thanks You

[@TINGANDYOU3399]

So I was following my lecturer's steps for the PyRx software, and i have encountered errors such as these: Error: list.remove(x): x not in list Error: Can't find Bable atom element for 'h from 4fm9 topo2a DDS I have sit in front of my pc for 6 hours already, and I try to seek help from lecturer, but he kept saying my protein has problem but he won't specify what's the problem. What can i do about this situation?

[@nidatanveer8328]

Thanks

[@samirasedehi5262]

Thank you for this video. I wish PyRx could offer students a special subscription rate for the software, similar to what PyMOL did.

[@akashmitrabiology]

Is PyRx paid nowadays? I haven't used it in a long time though

[@sabyasachibaksi2469]

It was very clear and conceptual

[@akashmitrabiology]

Glad I could help

[@asimadas5719]

Don't we need to remove the water molecules like it is done in autodock?

[@SBKHAN145]

hey akash, can i use autodock wizard in pyrx?

[@lateef230]

Dear , thanks for explaination, but I miss the step of converting pdb to pdbqt (macromolecule).was it done via bable software??

[@lateef230]

@@akashmitrabiology many thanks for replying. Please appoint that option since im too beginner Thanks again

[@salomanenicolaas6354]

This was very interesting indeed. I was wondering how do you prepare both your ligand and protein before docking?

[@lifeinsequence]

Thanks a lot for the video Akash! Very helpful. Though I've a doubt, when we download the structure of small molecules from PubChem, if there's no 3D conformer then can we dock our protein in 3D form with a 2D structure of our small molecule? Secondly how can I do site specific docking? Would be great if you suggest any video on that.

[@akashmitrabiology]

I am not so sure about how to perform sitr specific docking. And I don't think 2D conformers will work with a 3D model. I haven't tried it though. You can try it out and let me know.

[@sivaramansharadat3430]

How to dock peptide prepared t Through avogadro

[@akashmitrabiology]

Sorry i haven't used avagadro

[@sivaramansharadat3430]

@@akashmitrabiology how to dock peptides sir?