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

@sanketbapat

4 жыл бұрын

Thank you very much!

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

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

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

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

superb video..your way of explaination is so clear

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

This video series help me a lot

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

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?

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.

Very useful both parts for autodock vina learning

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

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

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

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

Honestly I appreciate so much your video thank you

Thanks for the amazing explanation

Very informative Sanket B.

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?

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

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 ?

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.

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

Thank you so much.

Very well explained sir

Thank you doctor🎉

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

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

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.

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?

Devudu swami nuvvu.. 🙏❤

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

@sanketbapat

4 жыл бұрын

Thank you very much!

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!

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

Amazing it's educating thanks

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?

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

4 жыл бұрын

from literature you have to search

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

I was done project work the same topic Sir.

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

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,

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??

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.

Sir thank you

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!

Thank you Sir

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

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

As we all know that docking simply interaction between receptor and ligand molecule, before docking we do remove the water molecule and some other additional ligands molecule , and add polar hydrogen bond also, Afer that we dock between receptor and ligand molecules, and more negative sign give the good stability.....but sir my question is that in natural condition how water and additional ligands remove from receptor molecules and how will i add polar hydrogen also?

Very nice information Dr. Gajanan Dongare Akola Maharashtra

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???

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 ?

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

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?

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..

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

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

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

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

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

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?

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

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

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

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 ?

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

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

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?

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

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

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

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

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.

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

I'm in bsc 2nd year and I could understand anything sir ... I'm just curious why did you remove the water molecules and add polar hydrogen to the protein ??

please sir .... teach me about cytoscape for beginners (tutorial),

Sir can u plz give tutorial on discovery studio ?

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

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

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 ?

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

Sir please can u name any inhibitor for hgd gene for alkeptonuria disease

Is there any rule regarding which chain should be kept and which one should be deleted ?

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

@_lemonny

3 жыл бұрын

Yes please!

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.

you are just pathfinder for bioinformatics learner.

in ligand prep you made an error ! ypu must do a torsion before save it as pdbqt

Before preparation both protein and ligand minimize step is important

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

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

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

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

I have installed autodock vina, but it is not working. would you please share the alternate link?

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?

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....

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

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

Sir, Amber 18 pe kaise simulation hota hai....iska video banaiye kabhi 🙏