Tutorial: site specific docking using auto dock vina.

This is a video tutorial version of the article found here bioinformaticsreview.com/2016...

[@vijaykrish7695]

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.

[@wylersonnogueira4168]

Thank you so much! Excellent tutorial, both video and article.

[@prayoga4419]

Thank you very much. This helped me a lot in my current research.

[@joaovitorfloridofranca9197]

Very good! Congrats, it helped me a lot in my molecular dynamics class! :)

[@ovalyadav]

Outstanding explanation mam...helped me a lot !!!!!

[@hasriatunpadmi1640]

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

[@r_chem335]

Can I do constraint docking (select key aminoacids for interaction in protein and ligand) in autodock vina? Thank you

[@cesaremartinelli4228]

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!

[@dishasharma7957]

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?

[@leoking3068]

Is there any need of energy minimization of ligand?

[@shivanipatel8405]

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.

[@intuitiveanatomyYT]

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?

[@rahulbhoi7121]

Are blind docking using Auto dock vina and then visualisation by pyMOL sufficient for new synthesized compounds? (About synthesis oriented research) Please suggest mam

[@GriffFredMc]

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!

[@Shubhamkumarzx]

How you are zooming up to visualise the GUI of autodock?

[@dheerajdube1128]

Thanks di!really helped me a lot

[@rsuiniurigutierrez4520]

Excellent video, where is the continuation for the result analysis? First of all, thank you!!

[@sumantakumar4330]

hello how to predict binding site of a protein ? thannx in advance

[@sheetalprajapati1522]

how do we get to know which chain we have to remove and keep?

[@lifesciencedecoded]

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

[@hasriatunpadmi1640]

It is mean that before we conducted spesifik docking we have to blind docking first, right?

[@saboor_saifi]

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!

[@wentingli4049]

So is force-field optimization necessary?

[@lailazahra3469]

A.o.a maam can u help me plz how install pathdock software

[@sumirankapur5998]

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??

[@rubembezerra1717]

Thank you very much for sharing the video.

[@worldfitnessgoal]

Mam specify a receptor before trying to write a grid dimension yeh likha aata h kya matlab h iska

[@user-rm4rp6lg4p]

What is the name of program which used in visualization

[@Biswabiology]

How to download and Install Autodock vina for windows 10 .. i need full process to download and instalation

[@nilimadas3466]

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

[@sameersingh2063]

you explained it so beautifully mam... thank you :)

[@essraaahmed276]

where did u write the last command plz at time 12:23??

[@haddouabdelghani6911]

Thank you so much.

[@amartya777]

is there any way to contact you? via email or something? I have a few questions which I would love to discuss.

[@dencelestra506]

Does this work for Protein-protein interaction as well?

[@manineeshrivastava586]

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?

[@snehakushwaha5177]

yes mam, u can do it either way

[@vinodraphael4281]

Good Tutorial

[@laibarajput3878]

how did you removed the chain B and lhead atoms pleaseeee reply

[@BilalAhmed-ib3yw]

you simply delete them either in notepad or selecting the chain you wants to deletw in the pymol.

[@meenalzala]

What command would you use to generate poses in Autodock?

[@shanmugapriyav.g3582]

u can use right arrow keys

[@manishupadhyay1017]

Its excellent and amazing maam i am using windows os how can i perform on that ?? please guide me....

[@manishupadhyay1017]

@Muniba Faiza Ok Thank you soo much ma'am. i'll try to it

[@ibrahimadiallo1020]

Thank you

[@arslanel1171]

Great thanks 😊

[@ramlingmali4002]

very nice video but I have question , how to generate configuration file ?

[@shanmugapriyav.g3582]

you need to create a new txt file and name it config. then type those info shown and save it

[@rahulmahapatra9401]

very useful video and very simply describe this. plz make some video about gromacs MD simulation. Thank you

[@chaserheinlander356]

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

[@harsharankaur4388]

command showing error

[@yaseenjanalchemist8026]

How to contact you ?? Please need help

[@bioinformaticsReview]

Send your queries at [e-mail]

[@isnarezqia7142]

Thank you.. may Allah bless you 🙏

[@user-xh3fz1ms7i]

good

[@GriffFredMc]

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

[@intuitiveanatomyYT]

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.

[@kitkatjp4724]

Horrible! :/