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

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Published 2020-03-20

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.

All Comments (21)

@harireddyresearcher540 4 years ago

thank u Sanket B.. excellent and more useful both of docking videos
@nipunivitharana1297 2 years ago

These two videos have been really helpful for my work. Thank you so much.
@ikshikasharely6106 5 months ago

I never thought i'll enjoy learning simulations so much. Thank you for making it so simple and easy. :)
@Princevx 2 years ago

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
@haideralmuqdadi5122 1 year ago

the best video i have ever watched so far thanks a lot for your kind efforts
@FarhanHaqj 3 years ago

You are doing a very good job. Keep it up Dr.
@sharvarikulkarni6045 3 years ago

superb video..your way of explaination is so clear
@Curious_Southerner 3 years ago

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?
@soulspeaks5231 3 years ago

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?
@kevingalindoherrera8315 3 years ago

It´s so nice your video, Sr! Thank you
@manasareddy7999 1 month ago

thank you sir , you explained each and every step very clear .
@ashrafwazir5037 3 years ago

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
@varalakshmiyadav8601 3 years ago

Very nice video sir.... Ur explanation was very clear ... Thanks a lot sir
@deniskalugin7984 2 years ago

Thanks for great tutorails! Small question - why do not you add all hydrogens but only polar ones?
@salaheddinehouache1015 3 years ago

Thanks for the amazing explanation
@sreevidyasankarasubramania733 1 year ago

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.
@shashwatkhuntia4439 2 months ago

This video series help me a lot
@hirenmarvaniya7264 2 years ago

Very useful both parts for autodock vina learning
@SufyanKhan-qv4js 2 years ago

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?
@iambond233 2 years ago

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