Thank you, Sir , for this insightful video. As a bioinformatics student, I found it extremely helpful in deepening my understanding of molecular docking. Your clear explanations and thorough guidance have been invaluable to my learning process. I truly appreciate your efforts in making complex topics easier to grasp
@mdamanat3611, I am planning the next two videos - One will be theoretical, to cover the concept of simulation, and why we need to perform..etc. The second one will be tutorial of simulation.
Thank you very much. Another nice tutorial. However, you have covered docking in so many tutorials, can you please make tutorial videos for molecular dynamics and DFT. I have made these requests several times in previous comment sections. Molecular dynamics especially for WINDOWS OS will be nice as well. Congratulations again.
@israelekoro8617 Dear, it is the time to make a series of Molecular dynamics simulations videos. I will cover it in different ways, just like i did with docking. Still, sorry for DFT, because i do not think that I am eligible to make a video on DFT. Once, i feel i can convey the concept, i will make not one but many. Best Regards,
Very well explained sir. I have one question sir. If I use my own GPU and RAM for molecular doxking , MD simulation, visualisation in SAMSON software using the Autodock vina extended extension and Gromacs extension. Can I do it for free? Or after 14 days of free trial for the extensions I have to pay?
Hello Sir, Currently I am learning pymol in this, i am comparing mutant and wild type protein to check how it function changes, My question is how can I know that because of the presence of this amino acid will have this function or thst function how can i say like that sir
@nirmalkumarkuppan6780 Dear, PyMol is primarily a visualizer. Referring to the second part of the question, that need an elaborative answer. Let me try.... Some of the proteins contain conserved catalytic residues that affects functional capabilities. So check it out. Also, to guide you, remember there are three basic role of amino acids in proteins. 1. Functional role 2. Structural role 3. No apparent role It is not necessary that a mutation will be directly important for a functional change. At times, it affects function through structural changes. To conclude try to look these points, 1. Is the mutation in active site? 2. If in active site, is it conserved at family level? 3. If yes, in point 1 or 2 above, now check the interaction details of that amino acid in wild and mutant. 4. Try to simulate both wild and normal. Concentrate of RMSF on that particular amino acid. If you see any differece, please discuss those potential affect. For example, you see that the mutant has attained opening or closure... Now this behavior can be discussed with the potential impact on function. I hope the above discussion will help you out. Cheers and thanks for watching
Thank you, Sir , for this insightful video. As a bioinformatics student, I found it extremely helpful in deepening my understanding of molecular docking. Your clear explanations and thorough guidance have been invaluable to my learning process. I truly appreciate your efforts in making complex topics easier to grasp
You are welcome to learn
Sir, will be eagerly waiting for your next tutorial. It was truly helpful.
My pleasure. Sure
You can also discuss about Moldy simulation application
So many topics are remaining, though I will try to cover. Thanks for the suggestion. :-)
Dear Sir, please make a video of Molecular dynamic simulation using Samson.
@mdamanat3611, I am planning the next two videos - One will be theoretical, to cover the concept of simulation, and why we need to perform..etc. The second one will be tutorial of simulation.
@@Bioinformaticsinsights Thank you Sir.
Thank you very much.
Another nice tutorial.
However, you have covered docking in so many tutorials, can you please make tutorial videos for molecular dynamics and DFT. I have made these requests several times in previous comment sections. Molecular dynamics especially for WINDOWS OS will be nice as well.
Congratulations again.
@israelekoro8617 Dear, it is the time to make a series of Molecular dynamics simulations videos. I will cover it in different ways, just like i did with docking. Still, sorry for DFT, because i do not think that I am eligible to make a video on DFT. Once, i feel i can convey the concept, i will make not one but many.
Best Regards,
Very well explained sir. I have one question sir. If I use my own GPU and RAM for molecular doxking , MD simulation, visualisation in SAMSON software using the Autodock vina extended extension and Gromacs extension. Can I do it for free?
Or after 14 days of free trial for the extensions I have to pay?
Thanks Dear, I would suggest to use institutional email in registration, even then if you need to pay after 14 days. It will be on a lower side.
Hello Sir, Currently I am learning pymol in this, i am comparing mutant and wild type protein to check how it function changes, My question is how can I know that because of the presence of this amino acid will have this function or thst function how can i say like that sir
@nirmalkumarkuppan6780 Dear, PyMol is primarily a visualizer. Referring to the second part of the question, that need an elaborative answer. Let me try....
Some of the proteins contain conserved catalytic residues that affects functional capabilities. So check it out. Also, to guide you, remember there are three basic role of amino acids in proteins.
1. Functional role
2. Structural role
3. No apparent role
It is not necessary that a mutation will be directly important for a functional change. At times, it affects function through structural changes. To conclude try to look these points,
1. Is the mutation in active site?
2. If in active site, is it conserved at family level?
3. If yes, in point 1 or 2 above, now check the interaction details of that amino acid in wild and mutant.
4. Try to simulate both wild and normal. Concentrate of RMSF on that particular amino acid. If you see any differece, please discuss those potential affect. For example, you see that the mutant has attained opening or closure... Now this behavior can be discussed with the potential impact on function.
I hope the above discussion will help you out.
Cheers and thanks for watching