Excellent work, Dr. Ashfaq! I was wondering-if we’ve already docked our protein using AlphaFold and are visualizing it in PyMOL, do we still need to run the script you mentioned in your video? Is there any option in PyMOL to isolate only the interacting residues, and also visualize in the figure? Thank you in advance!
Dear Masab, AlphaFold predicts the complex, but if one is interested to figureout what are the residues involved, for sure you will need PyMol or any other program to generate. You can watch the other videos regarding PyMol, I covered to learn about the selection process, and visualization. Also you can use PyMol as a plugin with Ligplot+, also you can use DS viewer or SAMSON. Best Regards
Hello Dr. Ashfaq. Thank you for the video. How about if i want to determine the driving forces such as hydrophobic or salt bride in the interacting portion?
Dear Osamika, thank you so much for taking interest in my videos. There are many servers and tools, but the best I can suggest is, pdbsum. Open this server from Google and then in the left side click generate. Upload your file, you will have results mentioning all the contacts. In a week or so, I will try to make a video tutorial of it also. Cheers
You need to first dock them. In case you want to follow my tutorial, here is the link. th-cam.com/video/-5s_EuS4cak/w-d-xo.html Once a docked complex is ready, you can use this Interaction video again.
hello sir, please can you guide how to measure the distance between two residues and how to label them in a protein-protein docked complex, there are a lot of videos related to the ligand and protein interaction, but its difficult to apply those in case of protein-protein docked complex
Most of my viewers are from biology background and they prefer GUI based stuffs. In case you like command based operations, please look to PyMol Wikipedia, all commands are listed with usage details. Regards
This is extremely helpful, Dr. Quick question, what happens if I already know the interaction sited between the 2 proteins? Can I give that to the script? Because I want to compare the interaction between 2 different proteins (2 different PDB codes)
@Julia if you the interaction interface exactly, then I suggest you to show those residues in PyMol. Why you want to tell the script the these two residues, the script is supposed to identify those two already. In case not then look to he script and tweak the cutoff distance, save and rerun. Yes you can identify between two different proteins, if they are in a complex. If they are individual proteins from PDB, in that case you have to dock them first.
Excellent work, Dr. Ashfaq! I was wondering-if we’ve already docked our protein using AlphaFold and are visualizing it in PyMOL, do we still need to run the script you mentioned in your video? Is there any option in PyMOL to isolate only the interacting residues, and also visualize in the figure? Thank you in advance!
Dear Masab, AlphaFold predicts the complex, but if one is interested to figureout what are the residues involved, for sure you will need PyMol or any other program to generate. You can watch the other videos regarding PyMol, I covered to learn about the selection process, and visualization. Also you can use PyMol as a plugin with Ligplot+, also you can use DS viewer or SAMSON.
Best Regards
Hello Dr. Ashfaq. Thank you for the video. How about if i want to determine the driving forces such as hydrophobic or salt bride in the interacting portion?
Dear Osamika, thank you so much for taking interest in my videos. There are many servers and tools, but the best I can suggest is, pdbsum. Open this server from Google and then in the left side click generate. Upload your file, you will have results mentioning all the contacts. In a week or so, I will try to make a video tutorial of it also.
Cheers
th-cam.com/video/AYll_iebwHE/w-d-xo.html
Excellent video! My question is, if I have two different sequences of proteins, how can I show the interaction between them?
You need to first dock them. In case you want to follow my tutorial, here is the link.
th-cam.com/video/-5s_EuS4cak/w-d-xo.html
Once a docked complex is ready, you can use this Interaction video again.
@@Bioinformaticsinsights thank you so much
Hello is there a script that can be used for visualization of interaction regions between several proteins in a model made by proteinix?
Dear, why not you are using the script in the video on different settings. Like first use it for chain A and B, then A and C, and finally B and C.
You have done great job
Thanks for taking interest. Please share it in your community, it might help some one else too.
hello sir, please can you guide how to measure the distance between two residues and how to label them in a protein-protein docked complex, there are a lot of videos related to the ligand and protein interaction, but its difficult to apply those in case of protein-protein docked complex
Here it is: th-cam.com/video/oWvvo4r2a68/w-d-xo.html
谢谢
You are welcome
Why you are using menu event to change the structure of protein. Why not command line argument. If you kindly do command line I will be helpfull
Most of my viewers are from biology background and they prefer GUI based stuffs. In case you like command based operations, please look to PyMol Wikipedia, all commands are listed with usage details.
Regards
This is extremely helpful, Dr. Quick question, what happens if I already know the interaction sited between the 2 proteins? Can I give that to the script? Because I want to compare the interaction between 2 different proteins (2 different PDB codes)
@Julia if you the interaction interface exactly, then I suggest you to show those residues in PyMol. Why you want to tell the script the these two residues, the script is supposed to identify those two already. In case not then look to he script and tweak the cutoff distance, save and rerun. Yes you can identify between two different proteins, if they are in a complex. If they are individual proteins from PDB, in that case you have to dock them first.