This was great, thank you! I hope you can help me with the below questions How do we analyze and find mutations and conformational changes in the protein because of those mutations and also if the mutations affect the protein-ligand interactions? How do we find out which binding sites have sites more affinity than the other?
Hello. Thank you so much for seeing the video. The simplest way to see a conformational change due to amino acid substitution is 'structural alignment' of the mutant protein to the wild type. You can always benefit of Uniprot.org to find out known mutations of a certain protein. If you wanna know amino acid substitution change the affinity of a ligand to the protein I suggest this video: th-cam.com/video/W1VG4c_5umk/w-d-xo.html. For your last question, to my knowledge, molecular docking is not the way for assessing a single amino acid affinity to a ligand or vice verse. This requires molecular dynamic simulation. I wish you best.
Dear Monika, if you want to manually highlight some certain residues do as follow: 1. Select a chain (optional) 2. From toolbar go to Favorits---> Sequence 3. Hold Ctrl and select residues in a chain 4. Go to Action and modify the selected residues. I hope you have fun editing. 👌
Your video is really useful, thanks 🙏🙏
Thanks for watching
باریکلا پسر
thank you for the video!!!
@Juan thank you for watching.
This was great, thank you! I hope you can help me with the below questions
How do we analyze and find mutations and conformational changes in the protein because of those mutations and also if the mutations affect the protein-ligand interactions?
How do we find out which binding sites have sites more affinity than the other?
Hello. Thank you so much for seeing the video. The simplest way to see a conformational change due to amino acid substitution is 'structural alignment' of the mutant protein to the wild type. You can always benefit of Uniprot.org to find out known mutations of a certain protein. If you wanna know amino acid substitution change the affinity of a ligand to the protein I suggest this video: th-cam.com/video/W1VG4c_5umk/w-d-xo.html.
For your last question, to my knowledge, molecular docking is not the way for assessing a single amino acid affinity to a ligand or vice verse. This requires molecular dynamic simulation. I wish you best.
How to manually highlight interactive residues? Everytime I try to label, it labels every redidue
Dear Monika, if you want to manually highlight some certain residues do as follow:
1. Select a chain (optional)
2. From toolbar go to Favorits---> Sequence
3. Hold Ctrl and select residues in a chain
4. Go to Action and modify the selected residues.
I hope you have fun editing. 👌