It's my pleasure to have your video tutorials sir, thank you for your efforts sir ! I kindly request you to please make video on KEGG pathway reconstruction for any protein/compound so I can understand the procedure .
Thanks a lot for your efforts to make bioinformatics user-friendly. I am from biotech background but bioinformatics though it was interesting but I was not able to understand by self study. Please update every chapter and new tools in this simplified tutorial.
Thank you very much for very insightful topic.... Kindly let me know how to interpret the results.. what if the score is very high and very low? What to say if it is very high and very low scores?
Hello sir.. Thank you for making such an informative video. I have a doubt. What is clustal size? In the FAQ section, clustal size was being asked to take into consideration rather than the binding energy while interpreting the result. Also can you please let me know what "members" denote in the result table?
I request you to make a video on How to use firedock server ASAP. Actually I am not getting how to get the transformation file , which is required in firedock.
Hello Sir. I tried protein-protein docking by ClusPro. But I got the results having chain A only although I uploaded separate Receptor and Ligand PDB files. Please help so that I can do the docking. As I said, only chain A is visible because ClusPro is "joining" the receptor and ligand pdb files.
Your explanation is nice.good job. I have one question can you please tell me the reference or picture courtesy of the protein- protein interaction which you showed in your cover slide before the explanation?
Hello sir very informative video. Sir, I want to dock wild-type and mutant RBD of Omicron Spike protein with ACE 2 receptor by cluspro. How can I do that? Please kindly ASAP. Thank you! Sir, also I have a macromolecule ligand 2s albumin and a model ligand flocculating protein and want to dock it with the mutant RBD Omiron S-protein-ACE 2 complex. How can I do that?
Hello sir very informative video. Sir, I want to dock wild-type and mutant RBD of Omicron Spike protein with ACE 2 receptor by cluspro. How can I do that? Please kindly ASAP. Thank you! Sir, also I have a macromolecule ligand 2s albumin and a model ligand flocculating protein and want to dock it with the mutant RBD Omiron S-protein-ACE 2 complex. How can I do that?
such a great efforts in making bioinformatics tools more easy to learn, thanks alot sir!
Truly appreciate the time you take and effort you make in your videos. So informative and helpful . Thank you Sir
It's my pleasure to have your video tutorials sir, thank you for your efforts sir !
I kindly request you to please make video on KEGG pathway reconstruction for any protein/compound so I can understand the procedure .
Thanks a lot for your efforts to make bioinformatics user-friendly. I am from biotech background but bioinformatics though it was interesting but I was not able to understand by self study. Please update every chapter and new tools in this simplified tutorial.
I want to appreciate you for this video, Thanks for this
Thank you so much for the tutorial video, Sir....
Thank you very much for very insightful topic....
Kindly let me know how to interpret the results.. what if the score is very high and very low? What to say if it is very high and very low scores?
Thanks for video. Can you explain what "members" in the table mean?
How can I create an account without using institutions mail ID in clusPro? I want to use it for my college project.
Informative video sir,thank you sir
Sir which one is better for protein-protein docking ..Haddock or ClusPro?
sir before that do we need to prepare our protein by adding polar hydrogen bond and removing water molecules ,checking for missing element?
Hello sir.. Thank you for making such an informative video. I have a doubt. What is clustal size? In the FAQ section, clustal size was being asked to take into consideration rather than the binding energy while interpreting the result. Also can you please let me know what "members"
denote in the result table?
Thank u so much for such an easy and helpful tutorial.
I request you to make a video on How to use firedock server ASAP. Actually I am not getting how to get the transformation file , which is required in firedock.
where can we convert any sequence into pdb format, suggest any website for converting into pdb; before submitting the sequence in cluspro.
Sir, could you please suggest a way by which i can so multiple protein protein docking at once as i want to dock different proteins with one protein.
May i know, what is the significance of binding scores from cluspro site?
Thank you for another informative video. Can you please make a video on how to dock multiple ligands to a single protein in pymol.
Hello Sir. I tried protein-protein docking by ClusPro. But I got the results having chain A only although I uploaded separate Receptor and Ligand PDB files. Please help so that I can do the docking. As I said, only chain A is visible because ClusPro is "joining" the receptor and ligand pdb files.
Your explanation is nice.good job.
I have one question can you please tell me the reference or picture courtesy of the protein- protein interaction which you showed in your cover slide before the explanation?
how to interpret in pymol ? and understand the scores ?
Hello sir very informative video. Sir, I want to dock wild-type and mutant RBD of Omicron Spike protein with ACE 2 receptor by cluspro. How can I do that? Please kindly ASAP. Thank you! Sir, also I have a macromolecule ligand 2s albumin and a model ligand flocculating protein and want to dock it with the mutant RBD Omiron S-protein-ACE 2 complex. How can I do that?
what is the difference between central score and lowest energy score??
Can cluspro be used for protein peptide docking?
Kindly make a video for Protein protein simulation
Sir, a great effort but i want to let everyone know that these scores should not be assumed as the binding energies or even binding capabilities.
Thank you, yes these are not binding energies, its a score derived from the formula which is based on energetics.
Hello, such a good comment. How can I calculate binding energy then? Thank you.
sir can we visualize clustpro result in dsv
No body mentions the importance of dock prep before uploading in clus pro. Is it not necessary?
Can you do molecular docking using pyrx software
how to analyze which residue interacting in the docking region?
Check protein-ligand interaction tutorial
Thank you.
Thank you so much
How to visualize the docked complex????
Pymol software
ua-cam.com/video/r6n15Zgbbig/v-deo.html pymol or use the software expalin in this video
Sir, kindly guide me on how to obtain pdb file for phosphorylated STAT3 protein.
Sir please help. I will be very grateful if you could help me.
Check Rcsb PDB for the protein
@@sanketbapat Sir it is in its complex form.
And I'm unable to obtain the phosphorylated form.
Please help Sir.
@@uzinidevi7670 You can save STAT3 as .pdb in Chimera. Then, add phosphorilation.
What exactly does these -ve energies are derived from? What are their in scientific units. Are these in kcal/mol?
Hi, You can always check paper for that. And I believe, most of these online tools reports desolvation, solvation energy.
جزاكم الله خيرا اخي الكريم 😂
Hello sir very informative video. Sir, I want to dock wild-type and mutant RBD of Omicron Spike protein with ACE 2 receptor by cluspro. How can I do that? Please kindly ASAP. Thank you! Sir, also I have a macromolecule ligand 2s albumin and a model ligand flocculating protein and want to dock it with the mutant RBD Omiron S-protein-ACE 2 complex. How can I do that?