Thank you so much sir for sharing knowledge and these videos are really very helpful for research scholars like us. 🙏😇 These tutorials are the best for pharmacy students working on molecular docking studies of newer drugs.
Dear Sir I am very much thankful and glad to you for this tutorial. Hope in future some extra knowledge regarding simulation and modeling tutorial will be seen. Thank you so much for this video.
Respected Dr. Ravikumar, I would like to thank you for sharing this wonderful step by step procedure. On the whole this video is very captivating and works as an ignition tool. I am curious and interested in learning it from the basics. Please give me advice.
Thank you for the tutorial video. Can you kindly upload a video on docking of metal complex (as ligand) using auto dock vina or auto dock 4.2? That will be very helpful.
Dear Mr Ravi, Thanks for the tutorial as it really helps me a lot! I hope you can help me answering these few questions cause I really start from zero in this area. I'm using the normal autodock procedure. How do I select the best conformation out of 100 runs? Should I focus the binding at the active site of protein to select?
Thank you so much for your video. Can I ask one question? How do I define exactly size x, y, and z because I see that it has a great effect on docked results?
thanks for making the docking procedure easy. it works well for me, i jjust want to know if we remove the exhaustivenss dose it has any thing to do with the simulation process.
Very interesting tutorial, very helpful video, very nice and simple method of explantion What are the ouput informations needed to be a publishable work?
Is the best bose the more hydrogen bonds no.3 or the highest affinity no.1. also, can we run the auto grid and auto dock from autodock tools will give the same results
Hi Sir, in the two version of autodoc tool, that mgtool website is offering, the line containing "Ligand- Flexible Residues-Grid-Docking-Run-Analyse" is missing. both versions- 1.5.6 and 1.5.7 both have the same issue; what to do? Open Babel can do this, but leaving some mistakes on which Autodoc vina refuses to operate. please help and Jai Hind.
This video is really helpful for me. I have one problem in the visualization by discovery studio. When i click on " show 2D diagram" it show 2D image , but the structure of ligand is not visualize as 2D; in this some heteroatoms are visible and another structure displayed as line. Pls sir solve this problem. Thankyou
Sir I am trying to perform site specific docking using autodock vina and define the grid box according to the residues but the problem is that instead of binding with selected residues in the grid box my ligand bind with other residues present in the grid box so pls tell me the solution for this?🙏🏻🙏🏻
hello sir i have done all the steps as u teach us in this amazing video but when i open my files in discovery studio it shows a very large distance between ligand and receptor as ligand is not going inside or on the surface of receptor plz help
Sir please make one tutorial on how to write Research article using this method and parameters obtained by it. Because everyone is giving tutorial of procedure of Docking but not writing the parameters in a proper way to publish an article. Kindly do as early as possible. It's an urgent need for everyone who is working in this field.
Something I've noticed is that hierarchy, remove water and hereoatoms may not be reliable. If you do that and save as a dsv file it retains the changes but if you save as a pdb and reopen the changes are not saved. I ended up removing mine with a pdb editor but I think you can do it manually. If anyone else has noticed this please let me know. Thanks Peter
Thankyou sir for making such a wonderful tutorial. I just have one question... Can I find active site xyz parameters using iitd site to make into conf text file ? Are they reliable for publication work?
Dear Dr. Ravi, I could do docking by following your procedure. But one of my compound has Pd metal. It is showing parameter not found. How can I update parameters for Palladium and proceed for docking by following same procedure. Thanks in advance
Sir whether in Chimera or in Pyrx... I'm able to find metal water/ligand interaction but while making a 2D structure in DS.... Saying that ligand is not in single format... How to solve or which visualizer to use?? TIA 🙏🙏
sir can you please tell me how much of score is considered as a good binding in the case of protein-peptide interaction? is there any threshold value? im getting -6.9Kcal/mol in the case of protein-peptide interaction.
Hello sir.. I have install the mgltools in local disk F.. in the video at 7.22 min you copied 3 files from vina folder... I have searched it in local disk F .. but unable to find it.. can you help me please
Here is the question, Please respond: I am running a molecule used as insecticides. How do I know which protein structure should be used in molecular docking?? My supervisor listed my to calculate the molecular docking as well but he has no idea about it either. Please can anybody provide me the research papers based on how to choose the protein to calculate the molecular docking structure ?
Sir when i save protein file it saves as autodock structure file and not as pdbqt file even after writing .pdbqt This happens with both target structure and ligand what should i do ??
Hello Sir. I tried downloading a file from RCBS. But unlike you I didn't get any option to choose file format. It automatically downloaded as a cif file. Kindly help.
i have seen many videos but trust me this is the best one !
thank you very much.
Thank you so much sir.... Best video for beginners... Explained in the best way.. Thank you so much
Thank you so much sir for sharing knowledge and these videos are really very helpful for research scholars like us. 🙏😇
These tutorials are the best for pharmacy students working on molecular docking studies of newer drugs.
are mazaaa aa geya video dekh bahut hi acha smjhaya u r such fantastic tutorial or jldi se multiple ligand k sath video bnaye sir....jai hind
Dear Sir I am very much thankful and glad to you for this tutorial. Hope in future some extra knowledge regarding simulation and modeling tutorial will be seen. Thank you so much for this video.
Again another highly useful class sir. Thank you
Thanks for your valuable feedback and support.
One of the best vidoe ever on docking.. Thank you so much Sir.
Respected Dr. Ravikumar, I would like to thank you for sharing this wonderful step by step procedure. On the whole this video is very captivating and works as an ignition tool. I am curious and interested in learning it from the basics. Please give me advice.
Thanku Sir..your explanation is amazing ..👍
it is one of the best video. Thanks for sharing.
Really nice tutorial. Thanks very much. 🙏
Thank you soo much sir, your doing great work 👍🏻
Thank you Sir. Thank you so much for this videos.
Thanks and nice presentation
Sir its very informative one first we do docking work in auto dock then for analysis we use discovery studio visualizer
thank you sir. i would like to clear some doubts regarding docking. i got error in center
-x constantly .i followed all your methods correctly
Thanks sir for presenting such excellent information with us
Thank you very much for the useful ppt... Highly appreciable
Amazing ! Simply Amazing Sir
Dhayanawad Bhava 🎉🎉
Great Job on the video. Please do keep our comments in mind. Many thanks
very helpful
Extremely useful tutorial. Thank you.
very nice presentation sir. thank you
Thank you for the tutorial video. Can you kindly upload a video on docking of metal complex (as ligand) using auto dock vina or auto dock 4.2? That will be very helpful.
Thanks again for another useful tutorial. I am expecting a tutorial on dynamics calculations with free tools.
Thanks for your support. Sure.
Is this method of docking preferable after obtaining the protein by homologous modelling?
Sir ur videos are very super.....take one class in Tamil for all these videos.
Dear Mr Ravi,
Thanks for the tutorial as it really helps me a lot!
I hope you can help me answering these few questions cause I really start from zero in this area.
I'm using the normal autodock procedure. How do I select the best conformation out of 100 runs? Should I focus the binding at the active site of protein to select?
Thanks for your support. U can select the best pose based on binding affinity, number of hydrogen bonds, and active site residues.
Thank you so much for your video. Can I ask one question? How do I define exactly size x, y, and z because I see that it has a great effect on docked results?
thanks for making the docking procedure easy. it works well for me, i jjust want to know if we remove the exhaustivenss dose it has any thing to do with the simulation process.
Excellent
very helpful Sir. Thank You Very MUCH
Excellent content
Keep guiding us sir🙏😊
Very interesting tutorial, very helpful video, very nice and simple method of explantion
What are the ouput informations needed to be a publishable work?
It was very helpful video, however I request you add a video by performing most of the steps using Autodock insted of Discovery studio
What about the attribute if protein pdb structure does not have ligand bound? I am in need of urgent help. Thank you.
If i have multiple ligands to be docked all for once, should i put all the ligands in the config txt file?
Sir, could you let me know if Autodock Vina is suitable for docking two proteins; antigen antibody
sir my protein has two chains and nearly ligands i dont know which to choose for the binding site
Good day to you sir. What is to be done if ligand profiles are not seen in the downloaded material from PDB.
Dear professor, thank you very much for the tutorial. Can you make a tutorial of docking with metal complexes as ligand?
You are a amazing
very good explanation sir how to dock green silver nanoparticles how to draw the structure of silver nanoparticles
Thank you so much for the video.
Can I follow the same procedure for docking multiple ligands??
Thanks for the video, Can you make protein protein interaction please
For this first we have to download auto dock software only or some other software needed
Is the best bose the more hydrogen bonds no.3 or the highest affinity no.1. also, can we run the auto grid and auto dock from autodock tools will give the same results
Hi Sir, in the two version of autodoc tool, that mgtool website is offering, the line containing "Ligand- Flexible Residues-Grid-Docking-Run-Analyse" is missing. both versions- 1.5.6 and 1.5.7 both have the same issue; what to do? Open Babel can do this, but leaving some mistakes on which Autodoc vina refuses to operate. please help and Jai Hind.
i have a doubt..from where to get the conf text file..?
Good explanation, if my pdb( protein) has no ligand, how to know grid position x,y,z etc and keep in conf.txt file, thanks
Thanks for your support. Select active site residues using grid and use those coordinates in conf.txt file.
Good explanation but I didn't get configuration file in MGL tools
hello sir
how to dock multiple ligands at a time using autodock ??
very nice demonstration , kindly help where we can find the config file. i cant find it in MGL tools.
you have to generate it I think
@@fozshub4915 you mean manually create the conf.txt file?
Very informative tutorial. What configuration is required for a PC to perform docking? Kindly reply.
Dear professor, can a ligand conformation be restricted while docking, i mean can a ligand be rigid?
Thank you very much.
This video is really helpful for me. I have one problem in the visualization by discovery studio. When i click on " show 2D diagram" it show 2D image , but the structure of ligand is not visualize as 2D; in this some heteroatoms are visible and another structure displayed as line. Pls sir solve this problem. Thankyou
hello, cant we do this in a simpler way by using only mgltools
good work
Thanks for your valuable feedback and support. Kindly share this with other researchers also.
Respected sir..the tutorial is very useful for beginners...i have a doubt..from where to get the conf text file..?
same problem
Plz make a video of protein-protein docking..
Thank u very much sir, can I know how to validation methode that you do to get good rmsd ?
a very good tutorial sir, but the autodock vina is unavailable to download, can you provide it?
can i use the same producer for DNA drug
Sir.. Thaks for tutorial.. How can i get of discovery studio client program
Sir I am not getting result after entering comand path after entering comand on second time
How do u label the residues in the 3D pose?
Sir I am trying to perform site specific docking using autodock vina and define the grid box according to the residues but the problem is that instead of binding with selected residues in the grid box my ligand bind with other residues present in the grid box so pls tell me the solution for this?🙏🏻🙏🏻
Good day to you sir. What is to be done if vina_split is not opening. Could you please help me out at this stage.
Got it Sir Thankyou.
great video ,, How can i do multi-Ligand in the same time using vina ??
Thanks for your valuable feedback. I will upload soon.
hello sir i have done all the steps as u teach us in this amazing video but when i open my files in discovery studio it shows a very large distance between ligand and receptor as ligand is not going inside or on the surface of receptor plz help
Sir please make one tutorial on how to write Research article using this method and parameters obtained by it. Because everyone is giving tutorial of procedure of Docking but not writing the parameters in a proper way to publish an article. Kindly do as early as possible. It's an urgent need for everyone who is working in this field.
Sir how to select a protein for a ligand
How to prepare ligand library of Zinc drug-like molecules (Natural Product and its derivatives)?
Sir pls upload a video using pmv instead of discovery studio
Something I've noticed is that hierarchy, remove water and hereoatoms may not be reliable. If you do that and save as a dsv file it retains the changes but if you save as a pdb and reopen the changes are not saved.
I ended up removing mine with a pdb editor but I think you can do it manually.
If anyone else has noticed this please let me know. Thanks Peter
Thankyou sir for making such a wonderful tutorial.
I just have one question...
Can I find active site xyz parameters using iitd site to make into conf text file ? Are they reliable for publication work?
S u can.
sir, im unable to install the discover studio tool. please help me, sir . it's very urgent for me regarding the project of my academics
Dear Dr. Ravi,
I could do docking by following your procedure. But one of my compound has Pd metal. It is showing parameter not found. How can I update parameters for Palladium and proceed for docking by following same procedure.
Thanks in advance
Can you help me? I have downloaded autodockvina but I am not able to run it.
Sir whether in Chimera or in Pyrx... I'm able to find metal water/ligand interaction but while making a 2D structure in DS.... Saying that ligand is not in single format... How to solve or which visualizer to use?? TIA 🙏🙏
i have the same problem. Did you solve it?
sir can you please tell me how much of score is considered as a good binding in the case of protein-peptide interaction? is there any threshold value? im getting -6.9Kcal/mol in the case of protein-peptide interaction.
Lesser the dock score better the pose. for eg: -11.098 is the best dock pose of all the other values like -9.856, 2.004
i have applied your method but vina is not runnning always getting error like this " Configuration file parse error: unknown option centre_x"
All fonts and icons in Discover studio visualizer are very small. How can I solve this problem
Tq sir
Sir, it's showing an error.... could not open log.txt for writing
Hello sir.. I have install the mgltools in local disk F.. in the video at 7.22 min you copied 3 files from vina folder... I have searched it in local disk F .. but unable to find it.. can you help me please
Download vina and install. Then u can find that files.
can anyone help me with this error "Configuration file parse error: unknown option protein"
i have a doubt..from where to get the conf text file..?
Sir, should we create a Configuration file?
It is a great video, how to dock morethan one ligands?
Thanks for your valuable feedback. I will upload soon. Kindly share this with other researchers also.
Hi Sir,
Configuration file parse error: unknown option receptop
I face this error when trying to run the cmd command
Here is the question, Please respond:
I am running a molecule used as insecticides. How do I know which protein structure should be used in molecular docking?? My supervisor listed my to calculate the molecular docking as well but he has no idea about it either. Please can anybody provide me the research papers based on how to choose the protein to calculate the molecular docking structure ?
Sir when i save protein file it saves as autodock structure file and not as pdbqt file even after writing .pdbqt
This happens with both target structure and ligand
what should i do ??
It will. Kindly follow the steps in video. Carefully.
I am trying to install Vina but I am having troubles to understand what to do, is there a tutorial that may guide newbies like me?
I will upload video for that.
Command prompt error i try many time sir but error came sir how to rectify sir
How to generate configuration file sir
i have a doubt..from where to get the conf text file..?
How to make that configuration file?
having the same doubt madam..did u find out..?
i have a doubt..from where to get the conf text file..?
Dear Sir,
How to proceed if the protein has multiple chains? Can i use all chains? I am a beginner sir but very much interested in docking studies.
It depends on the protein you choose
Hello Sir. I tried downloading a file from RCBS. But unlike you I didn't get any option to choose file format. It automatically downloaded as a cif file. Kindly help.
It will work sir.kindly try once according to the tutorial.