Thank you so much for the video tutorial. I have a questions: if a protein have two chains (chain A and B), for example BCL-2 with PDB entry 2W3L (Crystal Structure of Chimaeric Bcl2-xL and Phenyl Tetrahydroisoquinoline Amide Complex) and my target is Phenyl Tetrahydroisoquinoline Amide Complex. How we know Phenyl Tetrahydroisoquinoline Amide Complex in which chain? Please help
I know site-specific is a lot more efficient and faster than random docking, but I would still like to learn random docking protocols in case I'm facing a completely novel protein structure?
Hi, I followed the same steps but when I visualize the ligand in PyMOL I have only one state even if Vina has generated 8 models. I checked the pdbqt ligand file on a txt editor and in Autodock tools and it has actually 8 models inside. How come PyMOL visualizes only one of them? many thanks for your answer!
Maam mere binding energy pyrx virtual tool se -12.2kcal/mol aare h , but DSV se result analyse krne m unfavourable bumps, alkyl, vandevall interaction aese show hore hain.... To sir kya ye galat hai
How to delete hetatoms and other chains while keeping only one chain? Also, the file you got after clicking on download > PDB format, is different from what I got. I only got the 3D structure of protein which after clicking on it gets opened directly in pymol. How to download the file which you are showing the video?
UGH - frustrating - spent all afternoon setting up my programs, then my pdbqt files, then when I run the docking from terminal I get this: -bash: vina: command not found Any help?! Ready to smash something, lol!
my protein doesnot contain cl atom which is there in the ligand and maps are generated for all atoms in the protein. while autodocking its showing the error: I'm sorry; I can't find or open "@t" the atoms in protein are : A C H HD N OA SA and atoms in ligand are:A Cl OA N pls tell how remove the error
Hi, thank you for your video but I am facing an issue. I am using windows and with the command you provided, it is not reading the config file. It is showing vacant every time.
Are blind docking using Auto dock vina and then visualisation by pyMOL sufficient for new synthesized compounds? (About synthesis oriented research) Please suggest mam
I have a doubt. HETATM also represent water molecules. So, if i am removing it manually via text editor, then the step of removing water molecules via autodock is not required. Right?
Hello mam, I am trying to perform site specific docking as per ur procedure on windows using vina but the problem is that instead of docking with my selected residues the ligand combine with other residues in the grid box, I tried many times but failed due to this my result obtained is not as expected . So pls tell me the solution for this. Thank u!
How did you just randomly have a configuration file, should have been explained early in the video. Not many articles are mind enough to provide as in depth information as that
Everything was going good until 10:55 - then the train absolutely fell off the track 😂WTH happened? And here I thought I actually could do docking... SMDH
It might be helpful to briefly learn how to use command lines. Autodock Tools just preps you with pdbqt files and setting up configurations, but the actual Vina part is run on the command line. All you need to learn about command line is how to locate your files (cd) and make sure you downloaded vina properly, which differ by the OS you use.
madam you are such a great explainer. your lecture is awesome. i thought before see this video i cant do the docking. but now you maked its very easy.
where did u write the last command plz at time 12:23??
how do we get to know which chain we have to remove and keep?
Thank you so much for the video tutorial. I have a questions: if a protein have two chains (chain A and B), for example BCL-2 with PDB entry 2W3L (Crystal Structure of Chimaeric Bcl2-xL and Phenyl Tetrahydroisoquinoline Amide Complex) and my target is Phenyl Tetrahydroisoquinoline Amide Complex. How we know Phenyl Tetrahydroisoquinoline Amide Complex in which chain? Please help
I know site-specific is a lot more efficient and faster than random docking, but I would still like to learn random docking protocols in case I'm facing a completely novel protein structure?
How you are zooming up to visualise the GUI of autodock?
Hi, I followed the same steps but when I visualize the ligand in PyMOL I have only one state even if Vina has generated 8 models. I checked the pdbqt ligand file on a txt editor and in Autodock tools and it has actually 8 models inside. How come PyMOL visualizes only one of them? many thanks for your answer!
Maam mere binding energy pyrx virtual tool se -12.2kcal/mol aare h , but DSV se result analyse krne m unfavourable bumps, alkyl, vandevall interaction aese show hore hain.... To sir kya ye galat hai
It is mean that before we conducted spesifik docking we have to blind docking first, right?
Mam specify a receptor before trying to write a grid dimension yeh likha aata h kya matlab h iska
How to delete hetatoms and other chains while keeping only one chain? Also, the file you got after clicking on download > PDB format, is different from what I got. I only got the 3D structure of protein which after clicking on it gets opened directly in pymol. How to download the file which you are showing the video?
Hi... I am using autodock instead of vina version. So it will still give me the same result right? After that I can do it on pymol??
Can I do constraint docking (select key aminoacids for interaction in protein and ligand) in autodock vina? Thank you
UGH - frustrating - spent all afternoon setting up my programs, then my pdbqt files, then when I run the docking from terminal I get this:
-bash: vina: command not found
Any help?! Ready to smash something, lol!
Thank you so much! Excellent tutorial, both video and article.
Is there any need of energy minimization of ligand?
Outstanding explanation mam...helped me a lot !!!!!
hello
how to predict binding site of a protein ? thannx in advance
my protein doesnot contain cl atom which is there in the ligand and maps are generated for all atoms in the protein. while autodocking its showing the error: I'm sorry; I can't find or open "@t"
the atoms in protein are : A C H HD N OA SA and atoms in ligand are:A Cl OA N
pls tell how remove the error
Very good! Congrats, it helped me a lot in my molecular dynamics class! :)
Excellent video, where is the continuation for the result analysis?
First of all, thank you!!
Hi, thank you for your video but I am facing an issue. I am using windows and with the command you provided, it is not reading the config file. It is showing vacant every time.
Thank you very much. This helped me a lot in my current research.
Are blind docking using Auto dock vina and then visualisation by pyMOL sufficient for new synthesized compounds? (About synthesis oriented research)
Please suggest mam
What is the name of program which used in visualization
I have a doubt. HETATM also represent water molecules. So, if i am removing it manually via text editor, then the step of removing water molecules via autodock is not required. Right?
yes mam, u can do it either way
Hello mam, I am trying to perform site specific docking as per ur procedure on windows using vina but the problem is that instead of docking with my selected residues the ligand combine with other residues in the grid box, I tried many times but failed due to this my result obtained is not as expected . So pls tell me the solution for this. Thank u!
Does this work for Protein-protein interaction as well?
What command would you use to generate poses in Autodock?
u can use right arrow keys
So is force-field optimization necessary?
A.o.a maam can u help me plz how install pathdock software
How did you just randomly have a configuration file, should have been explained early in the video. Not many articles are mind enough to provide as in depth information as that
very nice video
but I have question , how to generate configuration file ?
you need to create a new txt file and name it config. then type those info shown and save it
how did you removed the chain B and lhead atoms pleaseeee reply
you simply delete them either in notepad or selecting the chain you wants to deletw in the pymol.
How to contact you ?? Please need help
Send your queries at muniba@bioinformaticsreview.com
How to download and Install Autodock vina for windows 10 .. i need full process to download and instalation
command showing error
Its excellent and amazing
maam i am using windows os
how can i perform on that ??
please guide me....
@Muniba Faiza Ok Thank you soo much ma'am. i'll try to it
is there any way to contact you? via email or something? I have a few questions which I would love to discuss.
you explained it so beautifully mam... thank you :)
Thanks di!really helped me a lot
Everything was going good until 10:55 - then the train absolutely fell off the track 😂WTH happened? And here I thought I actually could do docking... SMDH
It might be helpful to briefly learn how to use command lines. Autodock Tools just preps you with pdbqt files and setting up configurations, but the actual Vina part is run on the command line. All you need to learn about command line is how to locate your files (cd) and make sure you downloaded vina properly, which differ by the OS you use.
Thank you so much.
Good Tutorial
Great thanks 😊
Thank you
very useful video and very simply describe this. plz make some video about gromacs MD simulation. Thank you
Thank you very much for sharing the video.
Thank you.. may Allah bless you 🙏
good
Horrible! :/