Autodock Vina Tutorial | Protein preparation | Part-1

Protein preparation: parameters, protocols, and influence structure-based drug designing approach.
In the case of X-ray diffraction, this experimental strategy does not discriminate between electron density coming from static protein atoms or water molecules, meaning that most protein structures solved by X-ray diffraction also include so-called crystallographic waters (check the non-bonded red dots on the protein structure below). These molecules are not important for our particular docking simulation, and we also have to remove them.
6LU7: www.rcsb.org/s...

[@miow10]

Thank you so much for this tutorial!

[@ankita1301]

👍Keep up the great work. Gratitude for your vedioes !! Could you please help naïve beginners like me to understand metal, Zn complexed ligand docking… you wrote you will upload on metal docking too.. please do that.. I am in waiting….

[@alptekin6299]

1) Can all standard residues be removed by MGL tools? 2) Can we prepare the protein, (in the same way you did on chimera) by using MGL tools instead of using chimera? 3) and should we add kollman charges to all macromolecules? If depends, why?
I would really appreciate if you answer these questions because I couldn't find them anywhere
Good luck with your work!

[@BioinfoCopilot]

Yes absolutely 👍

[@alptekin6299]

@@BioinfoCopilot yes to all of them?

[@yaranour3396]

I compared the two files from the two different techniques but I fint that the pdb file generated by chimera has more charges than the pdqt file created by mgl tools

[@BioinfoCopilot]

Yes because in MGL tools you add hydrogens.

[@shubhedu.science3638]

It is very informative. One question... We can prepare protein by using Chimera or in MGL tool itself? right? what is better prepare in chimera and then use in mgl tool or direct prepare in mgl tool?

[@BioinfoCopilot]

Thanks! Both are having same functionality! Chimera gives a little more flexibility. Choose your own tool based on your preferences.

[@linhtruong7053]

Can I use Autodock Vina on Mac chip M1?

[@BioinfoCopilot]

Yes you can use Vina. But you can't install MGL tools. For that you need either linux or windows. You can use windows using docker in Mac. th-cam.com/video/xhGYobuG508/w-d-xo.html

[@user-ci7he2dr8f]

sir can you suggest me
i am molecular docking with selenium nanoparticles but it is not happening. also senps 3d structure is not available. and 1 more point that autodock is not running after update my system.

[@BioinfoCopilot]

Nanoparticles docking is another topic which I will cover when I reach 10K subscribers. Which OS you are using?

[@boorasanjit2013]

sir please make video on molecular dynamics simulation

[@BioinfoCopilot]

Yes sure!