You need to first dock them. In case you want to follow my tutorial, here is the link. ruclips.net/video/-5s_EuS4cak/видео.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
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 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.
ruclips.net/video/-5s_EuS4cak/видео.html
Once a docked complex is ready, you can use this Interaction video again.
@@Bioinformaticsinsights thank you so much
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: ruclips.net/video/oWvvo4r2a68/видео.html
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.