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PyMOL ligand-protein interactions | PyMOL tutorial | Protein Data Bank | Basic Science Series
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- Опубликовано: 12 авг 2024
- 00:00 Introduction
00:51 What we will Do Today
02:20 Publications
02:41 Note the code
03:03 Importing the Protein
03:14 Showing Chains
04:16 Removing The Water Molecules
04:29 Removing Other Chains
04:54 Removing Ligands
05:49 Showing Ligand
06:10 How to extract the Information
07:04 Hiding The Protein
07:36 Separating the sticks
08:21 Getting Information of the sticks
08:44 Changing into Residue
09:11 Extracting information of Polar-Contact Ligand Residues
09:55 Summary
11:21 Conclusion
PyMOL ligand-protein interactions
How to find Ligand Binding Pocket in PyMOL | PyMOL tutorial | Protein Data Bank | Basic Science Series
Keywords:
PyMOL protein ligand interactions,
PyMOL active site,
PyMOL ligand,
PyMOL polar contacts,
PyMOL H-bonds,
PyMOL residue distance,
PyMOL active site analysis,
PyMOL visualization,
PyMOL tutorial,
PyMOL ligand visualization,
PyMOL and Protein data bank,
PBD,
PyMOL protein structure,
PyMOL cartoon protein,
PyMOL ligand analysis,
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Your content and way of explaining is out of the world sir. Thanks a lot for clearing out long term doubt.
Thanks and welcome
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
Glad it was helpful!
it was so helpful that i immediately subscribed the channel!! sending love from Shanghai
Awesome! Thank you!
This is very helpful - thank you very much Professor!
Thank you so much!!
Thank you very much. It was really helpful and speeded up my work efficiency with PyMol
Glad it helped! Thank you for your valuable feedback!
oh my God. sir, I love you. everywhere else the instruction is so sparse and general. thank you !!!
Thank you so much for your kind support!
show sticks, byres all within 5 of ligand
For those who coudn't see the screen like me. copy paste this cmd
Use laptop if you want to watch the video it won't be helpful with mobile phones. Thanks for your comment 🙏🏼
@@BasicScienceSeries Can you make a video on how to calculate the volume of substrate binding site? Thanks in advance... :)
Thanks, it helps alot. English is not my first language, so it sounds unclear to me.
Thanks 😊
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."
Sure thing! Will do my best 🙏🏼Thanks alot 🙏🏼
Very clear - thank you
Glad it was helpful!
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
Will try to make more useful more, stay tuned for more 🙏🏻🙏🏻Thank you
thank you for this video
So nice of you
thank you, sir!!
Thanks for your comment 🙏🏼
thank you sir. everything is going well except when tap the bottom"S" at the underside bar no sequence information occured.
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.
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
Can you provide more details on the issue what command you are following ??
Good video. Fonts are too small.
Thanks will work on that 👍🏼
Can you do protein-protein binding affinity? Like binding sites of an antibody to a particular cell-surface protein?
Use cluspro server
Hello sir, how do we get XYZ coordinates of a particular ligand and it's interaction with other molecules on the PDB?
Use autodock tools
life saver
Thank you so much for your feedback!
i need to watch next part,,,
kindly provide me i haven't found
Soon, working on it.
Dear, what's the comand for select the residues close to the ligant? Thank you very much.
Check this on out, number of commands with examples: pymolwiki.org/index.php/Selection_Algebra
yes, since the picture is not clear enough to see 😢
Sir How to design anti drug conjugation
Please elaborate more
could you please write the command of show sticks you used
Mentioned in the video. Hope it helps.
The command is not clearly visible mention in the comments, please
Please check the comment section, if it is not posted already, let me know thanks 🙏🏼
when i select chain the ligand also selected i dont know why
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...
provide me link of next video
Soon!