Thank uuuuuu so much, sir... But one request sir. I'm a BS student of microbiology so I want to do an ms and PhD in bioinformatics. So I need more tutorials about the bioinformatics course and also the practical section too with each topic. Thanks once again 🤲
What are Gasteiger and Kollman charges? Where exactly are these charges being added in the protein? How can I determine the location of these charges in the protein
@@jiteshvdoshiDear prof, if after performing redocking, your ligand doesn't alignswell with the cocrystallised ligand, consequently doesn't gives you good RMSd value which parameters can you modify to have a perfect alignment with the cocrystallised ligand which will give a good RMSd value
This is awesome...sir I have question regarding it ...I'm doing work on Tubulin and MAPs in autodock vina software . When I am adding Hydrogen in Tubulin protein this shows a error of python shell. How will be it corrected?
Hi, I'll need to see the error to help you better. Often, of you read through the trace of the error, it takes you to the beginning of where the error originated. And most of the times, a clear reason will be given. With hydrogens, it may be an issue with missing atoms.. you can try repairing it from edit menu of autodock tools and see if it's works
It is hard to say for every protein, because at times, mutation at a distant site can also cause effect depending on protein's conformational flexibility and nature of mutation. In most common cases, and for standard docking, it may not cause any problems as we keep protein rigid. But it'll be good to find some literature about that specific mutation if it inactivates protein or not. If if does, there may be some changes in active site which you might need to correct.
Hi, unfortunately, there are no certificates for these webinar series. these are just learning exercises for who want to use these tools in their work.. we will keep you updated about certificate courses coming up soon
Awesome explanation, thank you very much! all the information is going to be very helpful for me
this is an amazing tutorial. thank you so much. subscribed and will share with friends.
Very clearly explained theory behind docking, not just the exercise part. I liked that a lot. Thanks for this webinar :)
Thank uuuuuu so much, sir... But one request sir. I'm a BS student of microbiology so I want to do an ms and PhD in bioinformatics. So I need more tutorials about the bioinformatics course and also the practical section too with each topic.
Thanks once again 🤲
What are Gasteiger and Kollman charges? Where exactly are these charges being added in the protein? How can I determine the location of these charges in the protein
Perfectly explained thanks, can you share the slides
This is wonderful, is it possible to have the slides used in this webinar
Sure, share your email id.
great!
Thank you so much Sir
Can you please make a video.in which is explained how adding a metal ion for docking?
Hello, yes i'll be making one soon! Thank you for suggestion.
@@jiteshvdoshi thank you very very much...for me is very important because I'm preparing the university thesis
amazing, but could you share the presentation please??
very clearly thank's
Sir please provide pdf of this session
What is the default spacing of vina? Is ut 0.375 or 1? Thank you
Depends on version of Vina. The earlier version (1.1.2) has default spacing of 1 while the latest version (1.2.*) has default spacing of 0.374
Creat and useful workshop
I am having problem in using autodocktools, as every time I add charge to hydrogen my tool automatically closes. I can't figure out whats the issue
Which university?
It was really nice and informative session.
Please share certificate link
Hi, unfortunately, there are no certificates for these webinar series. these are just learning exercises..
thanks alot sir for this amazing tutorial. concerning missing atoms if the missing residues are not in the binding site is there a need to model them?
If missing part of not in the grid box, you can work without them. But if you wish to perform MD later, it's good to model it
@@jiteshvdoshi thank you for the clarification
please an you explain how to calculate rmsd
Are you talking about RMSD between reference ligand and predicted pose? You can use match command in UCSF chimera for that
@@jiteshvdoshiDear prof, if after performing redocking, your ligand doesn't alignswell with the cocrystallised ligand, consequently doesn't gives you good RMSd value which parameters can you modify to have a perfect alignment with the cocrystallised ligand which will give a good RMSd value
This is awesome...sir I have question regarding it ...I'm doing work on Tubulin and MAPs in autodock vina software . When I am adding Hydrogen in Tubulin protein this shows a error of python shell. How will be it corrected?
Hi, I'll need to see the error to help you better. Often, of you read through the trace of the error, it takes you to the beginning of where the error originated. And most of the times, a clear reason will be given. With hydrogens, it may be an issue with missing atoms.. you can try repairing it from edit menu of autodock tools and see if it's works
My protein has mutation. But the mutation is far from the active site. Will it cause any problems?
It is hard to say for every protein, because at times, mutation at a distant site can also cause effect depending on protein's conformational flexibility and nature of mutation. In most common cases, and for standard docking, it may not cause any problems as we keep protein rigid. But it'll be good to find some literature about that specific mutation if it inactivates protein or not. If if does, there may be some changes in active site which you might need to correct.
Please provide feedback link for the same
Hi, you can send your feedback through email at hello@insightbioit.com
Is there certificate provided for this Webinar
Sir we havenot recieved Certificate of the Great Webinar...
Hi, unfortunately, there are no certificates for these webinar series. these are just learning exercises for who want to use these tools in their work.. we will keep you updated about certificate courses coming up soon
can u share the ppt?
Give me your email id