This is a video tutorial version of the article found here bioinformatics...
Пікірлер: 59
@vijaykrish76954 жыл бұрын
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.
@wylersonnogueira41683 жыл бұрын
Thank you so much! Excellent tutorial, both video and article.
@hasriatunpadmi16402 жыл бұрын
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
@prayoga44194 жыл бұрын
Thank you very much. This helped me a lot in my current research.
@sheetalprajapati15226 ай бұрын
how do we get to know which chain we have to remove and keep?
@joaovitorfloridofranca91973 жыл бұрын
Very good! Congrats, it helped me a lot in my molecular dynamics class! :)
@ovalyadav4 жыл бұрын
Outstanding explanation mam...helped me a lot !!!!!
@GriffFredMc4 жыл бұрын
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!
@intuitiveanatomyYT4 жыл бұрын
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?
@chaserheinlander3565 ай бұрын
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
@worldfitnessgoal Жыл бұрын
Mam specify a receptor before trying to write a grid dimension yeh likha aata h kya matlab h iska
@hasriatunpadmi16402 жыл бұрын
It is mean that before we conducted spesifik docking we have to blind docking first, right?
@rsuiniurigutierrez45205 жыл бұрын
Excellent video, where is the continuation for the result analysis? First of all, thank you!!
@cesaremartinelli42282 жыл бұрын
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!
@rahulbhoi71214 жыл бұрын
Are blind docking using Auto dock vina and then visualisation by pyMOL sufficient for new synthesized compounds? (About synthesis oriented research) Please suggest mam
@lifesciencedecoded3 жыл бұрын
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
@dishasharma79573 жыл бұрын
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?
@leoking30685 жыл бұрын
Is there any need of energy minimization of ligand?
@shivanipatel84054 жыл бұрын
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.
@sumirankapur59982 жыл бұрын
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??
@saboor_saifi4 жыл бұрын
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!
@nilimadas34664 жыл бұрын
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
@Shubhamkumarzx2 жыл бұрын
How you are zooming up to visualise the GUI of autodock?
@r_chem3353 жыл бұрын
Can I do constraint docking (select key aminoacids for interaction in protein and ligand) in autodock vina? Thank you
@essraaahmed2762 жыл бұрын
where did u write the last command plz at time 12:23??
@ibrahimadiallo10206 ай бұрын
Thank you
@sumantakumar43304 жыл бұрын
hello how to predict binding site of a protein ? thannx in advance
@sameersingh20635 жыл бұрын
you explained it so beautifully mam... thank you :)
@manineeshrivastava5864 жыл бұрын
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?
@snehakushwaha51772 жыл бұрын
yes mam, u can do it either way
@wentingli40494 жыл бұрын
So is force-field optimization necessary?
@user-rm4rp6lg4p3 жыл бұрын
What is the name of program which used in visualization
@dheerajdube11284 жыл бұрын
Thanks di!really helped me a lot
@Biswabiology4 жыл бұрын
How to download and Install Autodock vina for windows 10 .. i need full process to download and instalation
@rubembezerra17175 жыл бұрын
Thank you very much for sharing the video.
@lailazahra34694 жыл бұрын
A.o.a maam can u help me plz how install pathdock software
@dencelestra5062 жыл бұрын
Does this work for Protein-protein interaction as well?
@haddouabdelghani69114 жыл бұрын
Thank you so much.
@arslanel11712 жыл бұрын
Great thanks 😊
@vinodraphael42814 жыл бұрын
Good Tutorial
@meenalzala3 жыл бұрын
What command would you use to generate poses in Autodock?
@shanmugapriyav.g35823 жыл бұрын
u can use right arrow keys
@manishupadhyay10175 жыл бұрын
Its excellent and amazing maam i am using windows os how can i perform on that ?? please guide me....
@manishupadhyay10175 жыл бұрын
@Muniba Faiza Ok Thank you soo much ma'am. i'll try to it
@amartya7775 жыл бұрын
is there any way to contact you? via email or something? I have a few questions which I would love to discuss.
@ramlingmali40023 жыл бұрын
very nice video but I have question , how to generate configuration file ?
@shanmugapriyav.g35823 жыл бұрын
you need to create a new txt file and name it config. then type those info shown and save it
@rahulmahapatra94015 жыл бұрын
very useful video and very simply describe this. plz make some video about gromacs MD simulation. Thank you
@harsharankaur438810 ай бұрын
command showing error
@laibarajput38784 жыл бұрын
how did you removed the chain B and lhead atoms pleaseeee reply
@BilalAhmed-ib3yw4 жыл бұрын
you simply delete them either in notepad or selecting the chain you wants to deletw in the pymol.
@user-xh3fz1ms7i7 ай бұрын
good
@GriffFredMc4 жыл бұрын
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
@intuitiveanatomyYT4 жыл бұрын
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.
@yaseenjanalchemist80262 жыл бұрын
How to contact you ?? Please need help
@bioinformaticsReview2 жыл бұрын
Send your queries at muniba@bioinformaticsreview.com