Hello Dr. Majid! May i ask abut the ligand interaction with the receptor. How can we tabulate all the amino acid involved in the interaction between receptor and ligand with its type of interaction and distance?
When I try to display a 2D diagram of the ligand in Discovery Studio, I receive an error message saying 'Ligand is not a single fragment' and I don't know what I need to do. I need help to resolve this issue.
half video voice is not audible. Why you selected specific interaction. On what basis we decide which bond interaction to choose and which not to choose. In my structure their is metal and all interaction like in your structure. But why you deselected them?
Hello Dr Majid! Would you know how to convert multiple ligands from SDF to PDB format using BIOVIA studio? I figure out how to do it one by one, but it s taking too much time
If we have 100 ligands in single file SDF file, how can we convert all of them into 100 separate files of each ligand? If we have an option in DSV plz explain
@@MajidAli2020 respected sir why we want to convert all ligand in separate file... In dsv convert your ligand .dsv and the use this file directly by lib Dock method in dsv...
Jazak Allha kheren brother for this very clear demonstration. Thanks a lot
In that.. Protein we have ABABAB
SO please tell me which chains we have to cut?
Hello Dr. Majid! May i ask abut the ligand interaction with the receptor. How can we tabulate all the amino acid involved in the interaction between receptor and ligand with its type of interaction and distance?
Type of interactions and distance is available in the same software u can easily observe
Hello Dr Majid, i can not Install Discovery Studio Visualizer ,
Can you help me
Yes sure
@@MajidAli2020 Thankyou for your reply , how can me Install the Discovery Studio Visualizer
From google go to DSV and download its free version. Then install on ur computer
When I try to display a 2D diagram of the ligand in Discovery Studio, I receive an error message saying 'Ligand is not a single fragment' and I don't know what I need to do. I need help to resolve this issue.
Hello Dr. Majid kindly make a vedio on DNA protein interactions studies.
InshAllah
@@MajidAli2020 thanks Dr
Sir chimera not work on my hardware.In docking instead of it is rasmol can use
Yes
Sir, what version of discovery studio are you using?
2018 version
Is there any way or software to analyze protein-protein docking results. Kindly guide...?
You may consider same software for this. My tutorial is also available on protein protein interaction
@@MajidAli2020 link please?
half video voice is not audible. Why you selected specific interaction. On what basis we decide which bond interaction to choose and which not to choose. In my structure their is metal and all interaction like in your structure. But why you deselected them?
Depending on what kind of interactions are more likely to (similar to) co-crystallized ligand, stronger, and u can justify them
How to visualize the Pyrx docking output in DS? I got protein and ligand (dock positions) as separate pdbqt files. How to see them as complex in DS?
I have the same question
I will make video on that
in my ligand is not a single fragment sir, how can visualize the 2d diagram
Take each fragment separately
@@MajidAli2020 thank you sir, give me suggestion how to do that.
It needs more description, cannot explain in comment
Hello sir can you please share info about making animation in DSV?
Hello dr.please how can prepare Nanoparticles as ligand for autodocking
Difficult work, however if u know the size of particle and the number of atoms, u can try material studio for ligand prep
@@MajidAli2020 please can you write your email...I have article ..they prepared nanoparticles by Avogadro software
@@mohamedhamk3059 hm.ali6584@gmail.com
@@MajidAli2020 i sent email dr..please help mi?
Nice video, May I know what does unfavorable bump interactions means? Are they good or bad?
Bad, unfavourable for interaction at that region
Thank you so much Sir
nice video sir, may i ask how to move the label as we want?
Double click on label and move
@@MajidAli2020 thank you so much sir
Nice sir
Hello Dr Majid! Would you know how to convert multiple ligands from SDF to PDB format using BIOVIA studio? I figure out how to do it one by one, but it s taking too much time
One by one
you can convert all... its simple
If we have 100 ligands in single file SDF file, how can we convert all of them into 100 separate files of each ligand? If we have an option in DSV plz explain
@@MajidAli2020 respected sir why we want to convert all ligand in separate file... In dsv convert your ligand .dsv and the use this file directly by lib Dock method in dsv...
Dear, sometime we have a library of compounds in a single file and we need to separate each of these to minimize or some other purpose
Hello Sir, How to move the H-bond distance to the desired place? Is it possible?
No, it is not possible to increase or decrease the distance
@@MajidAli2020 Thank you for your comment. Is it possible to move the label of the distance?
@@DS-ry6pj you can remove it from here and rewrite by your own where u want in some other app like in paint etc.
@@MajidAli2020 Thank you very much.
use gview for this.
Great sir ♥️♥️
nice
Thanks
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Thanks
Hi, i have a question
Ask plz
visualization issue in software
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please would you repit all tutorials in arabic very slawly; that s very nteresting for me.
But I cannot speak arabic language. However, you can help me in learning arabic
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Sir how discovery studo downlode
I think I have mentione in one of my DSV videos
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You don't have check your video yourself.
I know there is voice problem
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