Thank you so much. I had been trying for two days to run command prompt but it always ended in an error. Your method helped to make it through. Thanks again.
@@Bioinformaticsinsightssir, after i visualize my docked structure on phymol, how i can download in pdb format? because once i download, i cannot find the pdb file of my docked structure in my laptop
@@puterielysaaliamohdbadri8974 Docking program has generated 9 pdbqt files. Now open pymol, click file then open a protein file in pymol. Again click file and open the pdbqt file. At the right bottom in pymol, you will see the play, and forward buttons. when you click the forward button, you see that the ligand orientation is changed. actually, when you click the forward button, among those 9 conformations, the next one is appeared. Now let suppose you are interested in some particular pose or orientation, keep that one in the screen. Now click the File, select the export molecule, and in the file type select the pdb, ent and name you file. click save. Your pdb is there where you have export it.
You are welcome. Dear @israelekoro8617, I did it with Pymol, I feel easy in Pymol. There are certain ways, you can even clean your protein directly from the protein file. Right click on the protein PDB and openwith in wordpad. Now manually select and remove, what you want to and save. Why I prefer Pymol? Because it offers a real time deletion or removing. It is easy, open your protein in Pymol. Click the "A" button in the right panel. Find, remove water at the bottom in the list. Click, water are removed. Also you can click on other things, you want to remove. Once selected, you will see a "sele" option. Click "A" button in front of the sele, and now click remove atoms. Done. Now click file, and save as. I have already made some videos on Pymol basic usage, still if you didn't get me... please let me know. Best Regards,
Thank you very much. I am so happy to come across your videos. You have rescued the science community from confusion. However, I have so many questions to ask about some of your other videos, I humbly request for an email address or any means to reach you. Thanks once again
Thanks for the complements. Although I am a very smaller entity, there are too many good people's in the field. Let's try this way. Send me your preferred time, if it suits me. I will arrange a live session on the channel. Everyone, can come with their questions or confusions. If you are not ok with it, drop ur mail here, I will contact you.
@@Bioinformaticsinsights Thanks once again. I will appreciate a video on application of DFT(Density functional theory) in drug discovery. I recently reviewed some literatures on molecular docking and drug design which contained the application of DFT. Since I'm a beginner in the field, I was lost in the discussion.
@@Bioinformaticsinsights Thanks once again. I will appreciate a video on application of DFT(Density functional theory) in drug discovery. I recently reviewed some literatures on molecular docking and drug design which contained the application of DFT. Since I'm a beginner in the field, I was lost in the discussion.
such informative tutorial... if you dont mind, can you make a docking tutorial for metal based compound... there are no tutorial on this in youtube yet
It means you are working in Linux or unix. Being a guest user, you can not write a file. To active a root, in your terminal write sudo su And enter It will ask for password. Type Now you will see hashtag sign, if yes ... You are on root. If not it means you type a wrong password
You can select your model of interest BUT if there is structure available in the PDB, then go for the PDB structure. In case you have many in the PDB, choose the one, with highest resolution. The lower the value, the higher is the resolution. Information of the resolution can be found on the PDB page for every structure.
When we do docking, at the terminal, it said: "swig/python detected a memomry leak of type 'BHtree', no destructor found", and then my docking stopped half way. What does that mean? And what should i do? I'm using windows 11, 64-bit system.
I can simply say that your python has some issues. Did you follow the installation protocols instructed in this video? if not, please have a try. If yes, then i am unable to help you on messages, as i do not know installation history of your computer.
Your message suggest that ligand structure is either corrupted or not discovery studio friendly. It better to save it in mol2 or pdb through openbabel. Then try to open, it will be fine. Openbabel is available in server mode
You will be able to find your ligand on Pubchem database. You can download it from there and then use Openbabel to convert it in your required formate, lets say (.mol2). Hope i have answered the question
Hey, I have a question. I'm planing research of transport of doxorubicyn with presence of Congo Red. I would like to know, can I make complex doxorubicyne with Congo Red as a way to create "protein" with ligand first and later can I use these "structure" like ligand for another calculation with cholesterol. So Can the original complex formed from doxorubicin and Congo Red be used as another "substitute" for simulations with cholesterol? I don't know, do you understand me? My english is not very good. Thanks for help and your video :)
@user-th6bv3kq2h Hi Dear, The docking methodology you watched is all about protein and compounds (ligands). In your question congo red and doxorubicin, both are compounds. You also mentioned transport. I assume your experiment also contain a transporter (protein). Therefore you will need to dock both the compounds with a protein separately (one by one). Only literature can tell you, the binding pocket of these two compounds. You also mentioned cholesterol, I again assume you mean building a membrane because transporters are present in a membrane. To summarize all the steps, you need to read literature. Find the binding region of congored and doxorubicin. Then bind both of them separately. Now build a membrane that will surround the docked protein (transporter). Proceed to simulation. Also prepare the same model but without congored. The model without congored will serve as a control and will tell you the impact of congored on doxorubicin. I hope this answer helps you. Best Regards
@@Bioinformaticsinsights Thank you so much. I'm just looking for others methods can I use in my master degree. Now I'm using Langmuir method in which I'm testing changes in π/A isotherms for cholesterol and two others lipids where Congo red solution is subphase or doxorubicyne solution is. I'm wondering about to use some like molecular modeling. I'm also thinking about DLS method, but I will prefer your idea. Thanks again!
It seems you are not using compatible wheel files with your python version. I suggest try to perform installation on python 3.10. Besides, there are some OS, like Chromebook, that do not support so many things. I will reply to your other comment, soon but that needs me to sit Infront of computer. Since last couple of days I am away.
@drjagadishdasari2294 Dear, if you have achieved this affinity score with AutoDock vina or AutoDock, then it seems fine. But remember to decide the better binding affinity you have to compare, normally with control ligand if any. In the case of no controlled ligand, researchers try to use number of different ligands, and comment on the best achieved pose. Also, if you have the setup, I will suggest to go for Simulation. Last, binding affinity is not the sole factor in publication, try to make a catchy story. Good luck
@@Bioinformaticsinsights Thanks lot ! I wanted to share that in my recent analysis, I found that one compound exhibits a binding affinity of -7.9 with human topoisomerase 1, while the other compound has a binding affinity of -7. This comparison provides valuable insights into the interactions of these compounds with the enzyme. hope in this way I can create story. once again thats a lot😀
@@Bioinformaticsinsights Thanks a lot by the way one last question how to fix....." swig/python detected a memory leak of type 'BHtree *', no destructor found"......in autodock the molecule is not visible while uploading ................
It is memory error, your computer is unable to allocate enough memory required for the process. It could be of many reasons, like there is a problem with your script, or ur computer hold insufficient free memory.
Dear I have already covered the tutorial of protein-protein docking and related visualizations. For protein-protein docking : ua-cam.com/video/5fNGn3tzBJE/v-deo.htmlsi=B1Ea1ApXNG6Utn15 you can also find the other videos to prepare handsome figures in PyMOL. Cheers
Dear sir you are doing great we are learning a lot from you here once again thanks for making bioinformatics in simple way
Good luck hasnain. All the best wishes
Thank you so much. I had been trying for two days to run command prompt but it always ended in an error. Your method helped to make it through. Thanks again.
Most welcome
omg thank you so much sir! your video is very helpful 💯
My pleasure and happy it helped you.
@@Bioinformaticsinsightssir, after i visualize my docked structure on phymol, how i can download in pdb format? because once i download, i cannot find the pdb file of my docked structure in my laptop
@@puterielysaaliamohdbadri8974 Docking program has generated 9 pdbqt files. Now open pymol, click file then open a protein file in pymol. Again click file and open the pdbqt file. At the right bottom in pymol, you will see the play, and forward buttons. when you click the forward button, you see that the ligand orientation is changed. actually, when you click the forward button, among those 9 conformations, the next one is appeared. Now let suppose you are interested in some particular pose or orientation, keep that one in the screen. Now click the File, select the export molecule, and in the file type select the pdb, ent and name you file. click save. Your pdb is there where you have export it.
@@Bioinformaticsinsightsomg it works! Thank youuu Dr 😭👍🏻
Thank you sir 😊😊
You are most welcome
Thanks so much.
At 6:01, did you clean the protein first using Discovery Studio?
That is, removing water molecules, heteroatoms, and the ligand.
You are welcome. Dear @israelekoro8617, I did it with Pymol, I feel easy in Pymol. There are certain ways, you can even clean your protein directly from the protein file. Right click on the protein PDB and openwith in wordpad. Now manually select and remove, what you want to and save.
Why I prefer Pymol? Because it offers a real time deletion or removing. It is easy, open your protein in Pymol. Click the "A" button in the right panel. Find, remove water at the bottom in the list. Click, water are removed.
Also you can click on other things, you want to remove. Once selected, you will see a "sele" option. Click "A" button in front of the sele, and now click remove atoms.
Done. Now click file, and save as.
I have already made some videos on Pymol basic usage, still if you didn't get me... please let me know.
Best Regards,
Thank you very much.
I am so happy to come across your videos.
You have rescued the science community from confusion.
However, I have so many questions to ask about some of your other videos, I humbly request for an email address or any means to reach you.
Thanks once again
Thanks for the complements. Although I am a very smaller entity, there are too many good people's in the field.
Let's try this way. Send me your preferred time, if it suits me. I will arrange a live session on the channel. Everyone, can come with their questions or confusions.
If you are not ok with it, drop ur mail here, I will contact you.
@@Bioinformaticsinsights Thanks once again.
I will appreciate a video on application of DFT(Density functional theory) in drug discovery. I recently reviewed some literatures on molecular docking and drug design which contained the application of DFT. Since I'm a beginner in the field, I was lost in the discussion.
@@Bioinformaticsinsights Thanks once again.
I will appreciate a video on application of DFT(Density functional theory) in drug discovery. I recently reviewed some literatures on molecular docking and drug design which contained the application of DFT. Since I'm a beginner in the field, I was lost in the discussion.
such informative tutorial... if you dont mind, can you make a docking tutorial for metal based compound... there are no tutorial on this in youtube yet
Sure, I will make a video for that, but I am trying to first complete the running course. Thanks for watching
Thank you 😊
Welcome!
Dr, what should I do if it says “please select root before writing file” when I prepare the ligand? 🥺
It means you are working in Linux or unix. Being a guest user, you can not write a file. To active a root, in your terminal write
sudo su
And enter
It will ask for password. Type
Now you will see hashtag sign, if yes ... You are on root. If not it means you type a wrong password
Which model should you select for docking ?
You can select your model of interest BUT if there is structure available in the PDB, then go for the PDB structure. In case you have many in the PDB, choose the one, with highest resolution. The lower the value, the higher is the resolution. Information of the resolution can be found on the PDB page for every structure.
When we do docking, at the terminal, it said: "swig/python detected a memomry leak of type 'BHtree', no destructor found", and then my docking stopped half way. What does that mean? And what should i do? I'm using windows 11, 64-bit system.
I can simply say that your python has some issues. Did you follow the installation protocols instructed in this video? if not, please have a try. If yes, then i am unable to help you on messages, as i do not know installation history of your computer.
Dr, how to do if i cannot visualize my 2D structure in biovia discovery studio because it says “the ligand is not a single fragment?”
Your message suggest that ligand structure is either corrupted or not discovery studio friendly. It better to save it in mol2 or pdb through openbabel. Then try to open, it will be fine. Openbabel is available in server mode
@@Bioinformaticsinsightsokayyy thank youu Dr 🙏🏻
Please what if the ligand you want to dock at the active site isn't on PDB database? Is there a way to get the 3D structure of any ligand? Thank you.
You will be able to find your ligand on Pubchem database. You can download it from there and then use Openbabel to convert it in your required formate, lets say (.mol2).
Hope i have answered the question
Can I perform docking if my ligand is Reactive oxygen species
Yes Jaspreet, you can, majority of the antioxidants retain the same principles.
Hey,
I have a question. I'm planing research of transport of doxorubicyn with presence of Congo Red. I would like to know, can I make complex doxorubicyne with Congo Red as a way to create "protein" with ligand first and later can I use these "structure" like ligand for another calculation with cholesterol. So Can the original complex formed from doxorubicin and Congo Red be used as another "substitute" for simulations with cholesterol? I don't know, do you understand me? My english is not very good. Thanks for help and your video :)
@user-th6bv3kq2h Hi Dear,
The docking methodology you watched is all about protein and compounds (ligands). In your question congo red and doxorubicin, both are compounds. You also mentioned transport. I assume your experiment also contain a transporter (protein). Therefore you will need to dock both the compounds with a protein separately (one by one). Only literature can tell you, the binding pocket of these two compounds. You also mentioned cholesterol, I again assume you mean building a membrane because transporters are present in a membrane. To summarize all the steps, you need to read literature. Find the binding region of congored and doxorubicin. Then bind both of them separately. Now build a membrane that will surround the docked protein (transporter). Proceed to simulation.
Also prepare the same model but without congored. The model without congored will serve as a control and will tell you the impact of congored on doxorubicin.
I hope this answer helps you.
Best Regards
@@Bioinformaticsinsights Thank you so much. I'm just looking for others methods can I use in my master degree. Now I'm using Langmuir method in which I'm testing changes in π/A isotherms for cholesterol and two others lipids where Congo red solution is subphase or doxorubicyne solution is. I'm wondering about to use some like molecular modeling. I'm also thinking about DLS method, but I will prefer your idea. Thanks again!
Please for reasons unknown to me pymol can't install in my computer after so many trials. How do I use discovery studio for the results analysis?
It seems you are not using compatible wheel files with your python version. I suggest try to perform installation on python 3.10.
Besides, there are some OS, like Chromebook, that do not support so many things.
I will reply to your other comment, soon but that needs me to sit Infront of computer. Since last couple of days I am away.
@@BioinformaticsinsightsOkay
Thank you
Sir how to downlod ions pdb file
Ions are located inside protein - when you download the protein PDB - you will have ions too
If a protein-ligand binding affinity is -7.9 is it ok to publish my results? kindly let me know
@drjagadishdasari2294 Dear, if you have achieved this affinity score with AutoDock vina or AutoDock, then it seems fine. But remember to decide the better binding affinity you have to compare, normally with control ligand if any. In the case of no controlled ligand, researchers try to use number of different ligands, and comment on the best achieved pose. Also, if you have the setup, I will suggest to go for Simulation. Last, binding affinity is not the sole factor in publication, try to make a catchy story.
Good luck
@@Bioinformaticsinsights Thanks lot ! I wanted to share that in my recent analysis, I found that one compound exhibits a binding affinity of -7.9 with human topoisomerase 1, while the other compound has a binding affinity of -7. This comparison provides valuable insights into the interactions of these compounds with the enzyme. hope in this way I can create story.
once again thats a lot😀
Yes, the difference is substantial. Good luck
@@Bioinformaticsinsights Thanks a lot by the way one last question how to fix....." swig/python detected a memory leak of type 'BHtree *', no destructor found"......in autodock the molecule is not visible while uploading ................
It is memory error, your computer is unable to allocate enough memory required for the process. It could be of many reasons, like there is a problem with your script, or ur computer hold insufficient free memory.
After running it’s says
This app can’t run on your PC
I DOWNLOADED 32 but my computer bit is that a problem
Please
As we execute autodock vina file in command prompt window, therefore, i suggest you to try 64-bit version of the program.
Thank you so much
You're most welcome
Sir , how to dock Protein with protein sir.
Dear I have already covered the tutorial of protein-protein docking and related visualizations. For protein-protein docking : ua-cam.com/video/5fNGn3tzBJE/v-deo.htmlsi=B1Ea1ApXNG6Utn15
you can also find the other videos to prepare handsome figures in PyMOL.
Cheers
i'ts work finaly
Happy to hear that. Good Luck