Molecular Docking Tutorial: AUTODOCK VINA - PART 1

Molecular Docking Tutorial: AUTODOCK VINA - PART 1 | Beginners to Advanced

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Күн бұрын

This is a Beginners to Advanced Level tutorial on Molecular Docking using AutoDock Vina software. Molecular Docking plays a critical role in Structure-based drug design and Molecular modeling. AutoDock is one of the widely used Bioinformatics tool for docking.
The software required for performing Autodock are mentioned below along with their link.
*AutoDock MGL Tools [mgltools.scripps.edu/]
*AutoDock Vina [vina.scripps.edu/downloads/]
*Pymol visualization tool [pymol.org/2/]
About the Lecturer:
Prof. Sanket Bapat completed his Ph.D. from the premiere CSIR-National Chemical Laboratory and the Biotechnology and Bioinformatics Institute, Pune. He worked as a project fellow in Haffkines Institute of Training, testing and Research, Mumbai where he worked on identifying target proteins in Swine Flu. Along with knowledge of statistical and biochemical techniques, he has also published several research papers in peer-reviewed journals and written a book chapter to his credit. Apart from research, he has a strong background in academic and institutional teaching experience.

Пікірлер: 222

@harireddyresearcher540 4 жыл бұрын

thank u Sanket B.. excellent and more useful both of docking videos

@sanketbapat 4 жыл бұрын

Thank you very much!

@Princevx 2 жыл бұрын

I think I'll put your name in acknowledgment, you are the only one who helped me in learning which I was roaming around behind everyone... Thanks

@ikshikasharely6106 7 ай бұрын

I never thought i'll enjoy learning simulations so much. Thank you for making it so simple and easy. :)

@nipunivitharana1297 3 жыл бұрын

These two videos have been really helpful for my work. Thank you so much.

@haideralmuqdadi5122 Жыл бұрын

the best video i have ever watched so far thanks a lot for your kind efforts

@sharvarikulkarni6045 3 жыл бұрын

superb video..your way of explaination is so clear

@FarhanHaqj 3 жыл бұрын

You are doing a very good job. Keep it up Dr.

@kevingalindoherrera8315 3 жыл бұрын

It´s so nice your video, Sr! Thank you

@007anildewani 4 жыл бұрын

Very informative Sanket B.

@hirenmarvaniya7264 2 жыл бұрын

Very useful both parts for autodock vina learning

@varalakshmiyadav8601 3 жыл бұрын

Very nice video sir.... Ur explanation was very clear ... Thanks a lot sir

@shashwatkhuntia4439 4 ай бұрын

This video series help me a lot

@manasareddy7999 3 ай бұрын

thank you sir , you explained each and every step very clear .

@salaheddinehouache1015 3 жыл бұрын

Thanks for the amazing explanation

@Eternitypunklove 4 жыл бұрын

hello, i find molecular dynamics hard to learn as i had no prior experience with coding and linux (what my teacher recommended me to use), videos like this makes it very easy for me to understand the concept and how to do it. THANK YOU FOR THE VIDEO!

@saherashraf1950 2 жыл бұрын

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@lovejeetsandhu585 4 жыл бұрын

Very well explained .. sir thankyou so much for ur efforts..

@sanketbapat 4 жыл бұрын

Thank you very much!

@iambond233 2 жыл бұрын

i want to give you the credit if I got a paper published like literally ...Extremely helpful

@ashrafwazir5037 3 жыл бұрын

Great tutirial and very informative one. Kindly if possible add ligand and DNA docking tutotrial. Sir it would be great job on your part. Thanks regards

@aalilouyoussra3365 Ай бұрын

Honestly I appreciate so much your video thank you

@rashamoustafa427 8 ай бұрын

Thank you doctor🎉

@sahriyanti6918 3 жыл бұрын

like your tutorial video sir, very helpful. Thank you so much 😇🙏

@vmkeditz7675 4 жыл бұрын

Very well explained sir

@joyceoliveira3916 4 жыл бұрын

Thanks for this video!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! I love you

@hafsatgarbamatsai7762 3 жыл бұрын

Amazing it's educating thanks

@haddouabdelghani6911 4 жыл бұрын

Thank you so much.

@Curious_Southerner 3 жыл бұрын

Sir, at 9:25 you add Kollman charges to the protein. However, at 15:23, when you load the protein macromolecule, you click on 'no' for preserving Kollman charges. The next popup box states that Gasteiger charges were added. So, should we add Gasteiger charges for the protein?

@mumbaimumbai6889 8 ай бұрын

Devudu swami nuvvu.. 🙏❤

@gajanandongare923 Жыл бұрын

Very nice information Dr. Gajanan Dongare Akola Maharashtra

@ushasingh9944 4 жыл бұрын

Sir thank you

@Sumitkumar-qs1mx 3 жыл бұрын

Thank you Sir

@deepakkarunakaran5217 4 жыл бұрын

Can anyone help me out with the installation , I seem to have problem with finding the vina folder in the path hence not able to attempt docking

@soulspeaks5231 4 жыл бұрын

Great job dear Prof. highly appreciated. I am quite new to molecular docking and trying to perform docking of activated carbon and a drug using your video as a guide. Will it be possible?

@namrithamaniyodath2877 3 жыл бұрын

Should we follow the default grid box dimensions mentioned in the autodock vina ? Wouldn't it be correct if we first checked literature for the docking site and then changed the dimensions of the grid box? Dr. Sanket , could you clarify this ?

@horanghae4649 2 жыл бұрын

Hi! Thank you very much. i learned a lot from your tutorial. May I ask, how can I specify the number of docking runs in Autodock Vina? Is it possible? Coz I am planning to dock at 70 runs.

@askntekin1709 2 жыл бұрын

you are doing grat job. Could you prepare a molecular docking video for ligand-based drug design.

@TheBiomics Жыл бұрын

At 17:55, Spacing parameter is set 0.375 A, but this is not used by AutoDock VINA. Changing this parameter affects the grid box size. So even you attempt to perform site specific docking, the docking is going to be blind docking due to this parameter. I am not able to get the clarification about this parameter while docking except VINA official tutorial has this option set as 1.

@kebarengrakau2450 4 жыл бұрын

Hi thanks for this, came at the right time! When adding the grid box, is it generated automatically at the binding pocket or will have to adjust it? if so, how do i ensure its the 'correct' coordinates?

@ashubehu 3 жыл бұрын

from literature you have to search

@deniskalugin7984 2 жыл бұрын

Thanks for great tutorails! Small question - why do not you add all hydrogens but only polar ones?

@koushalyajb2894 3 жыл бұрын

I was done project work the same topic Sir.

@sreevidyasankarasubramania733 Жыл бұрын

Thank you Sanket Bapat. Both the videos are very neatly and clearly presented. Highly informative. But once after docking how are we to interpret it in the paper. Any suggestions or advice regarding the same.

@pampamondal3912 4 жыл бұрын

Hello Sir! How to prepare script for multiple ligand docking?

@_lemonny 3 жыл бұрын

Yes please!

@truonghaminhnhat5227 3 жыл бұрын

If I use a receptor that I have already known the binding site with a reference ligand, how can I set the grid box in that binding site only for docking with other molecules?

@damiancastaneda7155 4 жыл бұрын

Thank you so much for your video Dr. Sanket. Firstly I hope you are healthy and safe. I'm trying to perform a molecular docking but I have an error while trying to save the PDBQT file: Unable to assign HAD type to atom Mg Unable to assign valence to atom protein:B: MG2003:MG type = Mg Unable to assign HAD type to atom Mg Unable to assign valence to atom protein:D: MG2003:MG type = Mg By any chance, do you know how to solve it? Thank you so much in advance!

@SufyanKhan-qv4js 2 жыл бұрын

Hi very informative tutorial on AutoDock Vina but I have a question which is that what about if we don't know about the ligand binding site of our protein so how can we set the grid?

@DrAkhtarAli08 Жыл бұрын

Hi Sanket, do you know how to calculate the binding constant or inhibition constant?

@constantinejohn3093 4 жыл бұрын

hello Dr Sanket. after running vina, Error: could not open "ligand.pdpqt" for reading. ligand is mol2 file format. how to turn it into pdpqt format?

@fenglitter7456 3 жыл бұрын

Hello Sir! thank you for your videos,i have a question ,when i drug the pdb files into Autodocktools software,it occurs a error “4mzi.pdb does not exists”,hope you can help me to solve this problem,thank you!

@user-qh3qm1lr3c Жыл бұрын

can anyone please explain my following question? this particular protein "4mzi" in this video has some missing residues in its side chain. so is it possible to do docking without fixing it ? in this mgl tool he didnt fix the missing residue. will that make good docking ?

@dipalibhalerao1658 4 жыл бұрын

you are just pathfinder for bioinformatics learner.

@lakshmisharoff5447 10 ай бұрын

Hi! Tab with Ligand icon not available to do ligand preperation in MGL tool. Appreciate your help regarding this how to go about

@DeekshaTare Жыл бұрын

Thank you for your helpful videos Dr. Sanket. I have a question. Is Autodock vina flexible or rigid docking?

@sreevidyasankarasubramania733 Жыл бұрын

Good day to you sir. Thank you for this excellent interactive session. I have a query, What is to be done if ligand profiles are not seen in the downloaded material from PDB.

@fahimalamnobel4789 4 жыл бұрын

if I follow the step by step of your docking lecture, then can i make the HLA/HLA-DBR and epitope docking properly for vaccine design??

@kavitaverma6322 2 жыл бұрын

It's very helpful can make a tutorial or multiple ligand docking and results interpretation on auto dock instead of pymol

@dhanuyendhe874 3 жыл бұрын

Hello sir, I'm from bioanalytical Sciences ... We had your workshop that I couldn't attend because of personal problems n we have this docking by autodock vina in our practicals n we have our practicals from 8 ... N I'm having some major issues... Whenever I try to download protein it gets downloaded in rasmol raswin than pdb extension .... N ligand in sdf where it supposed to be downloaded in MDL sdf format n because of it I'm not able to proceed ... Can you please suggest me what can be done ?

@vidyavaishnavi7723 3 жыл бұрын

Sir few docking files in the folder remain hidden and no matter what I do, I'm not able to view them in the Docking folder. It's visible in AutoDock when I select Read Molecule but not in the folder. How do I resolve this sir?

@ebtihalabdullah3720 3 жыл бұрын

i use pyrx for docking, and use multiple ligands i download them from zinc database (nubben database for natural compounds), i do minimization and docking but when finish the result are encodede for the compound it just codded the energy , and they are 2332 compound how can i know the compound crosspend to each result???

@moumitachakrabarti6424 4 жыл бұрын

Hi! very helpful video indeed. I have one query which is my SDF file is not getting recognized as a SQLCE database. how do i overcome this error? Kindly help..

@pallabimustafi8699 3 жыл бұрын

Hey very nice and clear presentation. Wanted to ask one question so the final poses that you visualise in pymol and if we suppose find the first pose as the best docking pose how do we save it and use for showing it in power point?

@sanketbapat 3 жыл бұрын

You can download the pdb file of the first pose, and then take an image of it.

@dipalibhalerao1658 4 жыл бұрын

sir can you please tell me how to determine mutation rate of covid19 using bioinformatics tool? and which tool can be used?

@lopamudrasahoo4646 4 жыл бұрын

Sir plz make a video of docking by arguslab ...i really need it now

@lifesciencedecoded 3 жыл бұрын

sir same dimensions rakhne main result alag alag kyu aata hai, jese maine ek ligand ke liye dimension x, y, z 30,40,50 rakhi or binding energy 10 aare h autodock vina se, but jab main yahi dimension rakhta hu same lifand ke liye, par is time main pyrx virtual screening tool se karta hu to result 9 binding energy kyu aata hai

@rohitchel5679 2 ай бұрын

Im performing docking on a known active site so i limited the gridbox around the active site only. Some of the conformations i got after docking were outside the grid box. Is that normal?

@nilimadas3466 4 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 "5nm2.Cl.map" 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

@shanavazh2341 4 жыл бұрын

Respected sir need help The command shows the program is not recognized as an internal or external command operable program or batch file what is the solution for this problem

@fareehatahir1279 2 жыл бұрын

It is necessary in autodock to kept the torsion agnles of ligand less than 6?

@fozshub4915 3 жыл бұрын

Cant I do docking in the autodock tool instead of prompt command?

@sonuverma1901 4 ай бұрын

Sir, can we used ligand file prepared in autodock tool in Vina and what about energy minimization step?

@lifesciencedecoded 3 жыл бұрын

Cyp 17 ko pyrx virtual screen tool main upload karne se alternate conformation bata raha hai, or pdbqt file main convert nahi ho raha hai....

@RakeshBhowmick 3 жыл бұрын

Can DNA-Protein docking be performed in Autodock? Please suggest a suitable tool for building DNA 3D structure

@kirtisharma6531 3 жыл бұрын

Hello sir, when i click on grid and selecting the protein then get error, showing protein pdbqt has one or more hydrogens with no bonds. Plz solve this problem

@ashubehu 3 жыл бұрын

Hi Sanket in Ur video you have not mentioned the path of folders where we must keep the files to run autodock, when I am running auto dock it showing error

@sanketbapat 3 жыл бұрын

If you see the video I had created the folder on Desktop, you can create your destination folder anywhere you want.

@eshwarb2489 3 жыл бұрын

Hi, I have a issue. I'm not able to get docking results as it show error like, FATAL ERROR: ERROR: 3778 records read in, but only dimensioned for 2048. Change "MAX_RECORDS" in "constants.h". Can u please suggest how to rectify this error ?

@fnpereirajunior 3 жыл бұрын

thanks for the video!!! how can i choose only the active site of the protein to do the docking? and how to find out where the active site is?

@cpu5888 3 жыл бұрын

use castp

@sazan447 Жыл бұрын

Sir, I downloaded autodock-vina from the link but after installing the program, it does not have the brown ribbon you used to save the protein and ligand, what should I do?

@uzinidevi7670 3 жыл бұрын

Sir, please reply on how to get a pdb file of phosphorylated STAT3

@saikatmandal929 3 жыл бұрын

Can we perform docking with metal complexes ( Pt complex)?

@guglielmomontarani5048 3 жыл бұрын

Sir, very nice video Can you please make a video in which you explain how adding a metal ion ( in my case is tin)

@saikatmandal929 3 жыл бұрын

I am facing problem for adding pt metal.

@guglielmomontarani5048 3 жыл бұрын

@@saikatmandal929 I understood that you don't have to use vina.exe but directly autogrid4 and autodock 4 on autpdock tool. But when I try to put the new parameters the program doesn't run

@lifesciencedecoded 3 жыл бұрын

Sir suupose hum ek research article likh rahe hain , sir kya hum comparison ke liye aesa kar sakte hain kya, jese remdesivir ke liye dimension xyz alag rakh rahe hain isme humne docking autodock vina , command prompt waale step se docking ki , or other multiple ligands ke liye humne autodock vina , command prompt se docking nahi ki more than two ligands hone ke usse , isme humne pyrx virtual screening ka use kiya or dimension xyz bhi different rakhi as compare to remdesivir... To sir kya hum comparison kar sakte hain ab remdesivir or ye multiple ligands kaa.... Yaa hume sabhi ligands ke liye pyrx virtual screening he krni pdegi , agar hum research article m isko publish karana chahte hain to.... Sir koi problem create to nahi hogi dimension different rakhkr comparison kiya karkr

@oyephotographer 5 ай бұрын

My pdb file is getting downloaded in the form to words how can I get in form of image

@diptendusarkar1912 3 жыл бұрын

if some non bonded atom remain your protein, then how to remove them?

@ishadaxini8120 11 ай бұрын

Hi Dr. Sanket. I am an IBDP 2 student. For my school project I need to conduct multiple ligand simultaneous docking. I was able to conduct single ligand docking but am unable to understand how to do MLSD. Can you please help with instructions on how to do this. Thank you

@justsomething...9353 3 ай бұрын

I have a doubt. I guess The grid box has to be formed around the active site residues by changing the x, y and z axis values so that the interaction can be calculated correctly,

@user-lz3op3nw2p 3 ай бұрын

my protein file is not saveing as the pdbqt so what should i do

@aniketh8 4 жыл бұрын

i am looking for PDB file of Beta Amyloid Protein (Alzheimer's Disease) can anybody help please.

@aruna3234 4 жыл бұрын

Whenever I open a pdb file ,a popup appears regarding the file format not being supported by the system. Do we require any other application in order to view the pdb file? If so please tell which one.

@sanketbapat 4 жыл бұрын

You can download Pymol and open the PDB file in it.

@ayushiagarwal411 3 жыл бұрын

Can you please let me know why do we add polar hydrogens and kollman charges?

@rashamoustafa427 8 ай бұрын

What about chimera or autodock and pymol is more effective...thank so much Dr.sankat🎉🎉😊

@Aambo04 Жыл бұрын

I am not getting the grid option in my Python molecule viewer. Can anyone tell me, how to get it?

@snehakushwaha5177 2 жыл бұрын

Thank you sir for such a nice video. One question- if we don't know the active site, why we are not enclosing the whole protein inside the grid by changing dimensions.?

@sanketbapat 2 жыл бұрын

Good question, yes we can encompass the whole protein.

@mefunkyana2210 4 жыл бұрын

Hello Sir, had a doubt regarding protein preparation. What are we suppose to do when a dialogue box appears saying "Found non bonded atoms" ? Do I ignore it and save the protein anyway or is there a separate step for it? Also wanted to let you know that I found this tutorial extremely useful Thanks!

@ultron7045 Жыл бұрын

Same issue, what should I do?

@pallavisangle4787 3 жыл бұрын

In docking...grid macromolecule protein are choose..then show error....so, what do i do now.... Plss..help me..

@joyceoliveira3916 4 жыл бұрын

Could you make a video showing how to dock in Vina Auto-docking using some flexible active site waste? I need my molecule to interact with specific residues and I don't know how to do it. Please.

@ashubehu 3 жыл бұрын

Hi joyce I think you cover all the protein by doin grid box so it will be flexible as you took all protein whereever will get less energy it will enter

@ultraprotitan466 3 жыл бұрын

Thanks for such a nicely presented video, especially for beginners. However, during the protein and ligand preparations, i am unable to save file in pdbqt format. kindly guide through some tips, which could work for me

@dilkashgazala831 2 жыл бұрын

Same with me sir, please guide us.

@anupamaroy8893 4 жыл бұрын

Can you please guide with homology modelling using Modeller???

@zoilagandara5726 4 жыл бұрын

when you get the nine possible conformations which you choose from them, are they all valid or is the first?

@sanketbapat 4 жыл бұрын

All are valid comfirmations but the best docked is first

@rohanpawar2891 3 жыл бұрын

Sir,can you tell how to determine ki for inhibitors using autodock

@deepsikhaaa7816 2 ай бұрын

sir I wanted to know..if the same thing can be executed in ubuntu system

@sukhamoyg 2 жыл бұрын

Is it possible to do docking without keeping the the AD4.1_bound.exe, AD4.1_parameters.exe and autodock4.exe, autogrid4.exe files in the same working folder?

@sanketbapat 2 жыл бұрын

Yes its possible, even my working folder doesn't have the executable file