Molecular Docking Tutorial: AUTODOCK VINA - PART 1 | Beginners to Advanced
236,083
Published 2020-03-20
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)
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thank u Sanket B.. excellent and more useful both of docking videos
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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
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These two videos have been really helpful for my work. Thank you so much.
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I never thought i'll enjoy learning simulations so much. Thank you for making it so simple and easy. :)
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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?
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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.
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Thanks for great tutorails! Small question - why do not you add all hydrogens but only polar ones?
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the best video i have ever watched so far thanks a lot for your kind efforts
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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
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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.
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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?
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Thank you for your helpful videos Dr. Sanket. I have a question. Is Autodock vina flexible or rigid docking?
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thank you sir , you explained each and every step very clear .
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superb video..your way of explaination is so clear
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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 ?
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You are doing a very good job. Keep it up Dr.
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This video series help me a lot
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Hi! Tab with Ligand icon not available to do ligand preperation in MGL tool. Appreciate your help regarding this how to go about
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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!
