PyMOL ligand-protein interactions | PyMOL tutorial | Protein Data Bank | Basic Science Series

[@Shadow-bx8ri]

Your content and way of explaining is out of the world sir. Thanks a lot for clearing out long term doubt.

[@BasicScienceSeries]

Thanks and welcome

[@Amir-jn5mo]

Amazing video. I had no clue what to even do in pyMOL as it looked intimidating. Now I can easily clean up a protein and focus on presenting the binding pocket im interested in

[@BasicScienceSeries]

Glad it was helpful!

[@egowong317]

This is very helpful - thank you very much Professor!

[@BasicScienceSeries]

Thank you so much!!

[@arshiaamjad9220]

it was so helpful that i immediately subscribed the channel!! sending love from Shanghai

[@BasicScienceSeries]

Awesome! Thank you!

[@manishmishra9177]

show sticks, byres all within 5 of ligand For those who coudn't see the screen like me. copy paste this cmd

[@BasicScienceSeries]

Use laptop if you want to watch the video it won't be helpful with mobile phones. Thanks for your comment 🙏🏼

[@manishmishra9177]

@@BasicScienceSeries Can you make a video on how to calculate the volume of substrate binding site? Thanks in advance... :)

[@ikaoktavianawati4736]

Thanks, it helps alot. English is not my first language, so it sounds unclear to me.

[@adampruska1738]

Thank you very much. It was really helpful and speeded up my work efficiency with PyMol

[@BasicScienceSeries]

Glad it helped! Thank you for your valuable feedback!

[@bangnikabang6501]

oh my God. sir, I love you. everywhere else the instruction is so sparse and general. thank you !!!

[@BasicScienceSeries]

Thank you so much for your kind support!

[@vigneshpandi5722]

Thanks 😊

[@marufislam3777]

Thank you so much, sir. Can we get more tutorials as you said in this video? Like: "Finding the residues in the ligand binding pocket."

[@BasicScienceSeries]

Sure thing! Will do my best 🙏🏼Thanks alot 🙏🏼

[@robertmuller1881]

Very clear - thank you

[@BasicScienceSeries]

Glad it was helpful!

[@vamsivardhan5403]

The tutorial was absolutely fantastic and made to involve more but I could not find the link for the continuation of this video regarding labelling for each residue,, can anyone share the continuation of this video link plzz

[@BasicScienceSeries]

Will try to make more useful more, stay tuned for more 🙏🏻🙏🏻Thank you

[@matthewadihonneyamos8723]

thank you, sir!!

[@BasicScienceSeries]

Thanks for your comment 🙏🏼

[@imenfathallah5788]

thank you for this video

[@BasicScienceSeries]

So nice of you

[@sarinasarina3973]

thank you sir. everything is going well except when tap the bottom"S" at the underside bar no sequence information occured.

[@BasicScienceSeries]

So nice of you : ) Thank you so much for your kind support and for your comment as well.. It should work if you are not able to get the sequence, try reinstalling the software again.

[@Fordance100]

Good video. Fonts are too small.

[@BasicScienceSeries]

Thanks will work on that 👍🏼

[@israthumayunslifeinchina4996]

show sticks, by res all within 5 ligand i was write according to your information but residues not coming, in your video it is also not clear, can you please give me detail

[@BasicScienceSeries]

Can you provide more details on the issue what command you are following ??

[@Yellownealy]

Can you do protein-protein binding affinity? Like binding sites of an antibody to a particular cell-surface protein?

[@BasicScienceSeries]

Use cluspro server

[@luluingram3735]

life saver

[@BasicScienceSeries]

Thank you so much for your feedback!

[@dhruvipatel4144]

Hello sir, how do we get XYZ coordinates of a particular ligand and it's interaction with other molecules on the PDB?

[@BasicScienceSeries]

Use autodock tools

[@fatimagenetics]

i need to watch next part,,, kindly provide me i haven't found

[@BasicScienceSeries]

Soon, working on it.

[@waqi409]

The command is not clearly visible mention in the comments, please

[@BasicScienceSeries]

Please check the comment section, if it is not posted already, let me know thanks 🙏🏼

[@karenluiselang3423]

Dear, what's the comand for select the residues close to the ligant? Thank you very much.

[@BasicScienceSeries]

Check this on out, number of commands with examples: pymolwiki.org/index.php/Selection_Algebra

[@ikaoktavianawati4736]

yes, since the picture is not clear enough to see 😢

[@amalelfoly5944]

could you please write the command of show sticks you used

[@BasicScienceSeries]

Mentioned in the video. Hope it helps.

[@alchemista947]

when i select chain the ligand also selected i dont know why

[@BasicScienceSeries]

Thank you so much for your kind support and for your comment as well.. You need to select the residue option not the chain option at the bottom of the right corner. Play around I am sure you will figure it out. Which molecular you are exploring...

[@aneeshaanilkumar3935]

Sir How to design anti drug conjugation

[@BasicScienceSeries]

Please elaborate more

[@fatimagenetics]

provide me link of next video

[@BasicScienceSeries]

Soon!