Protein-ligand docking with AutoDock Vina and UCSF Chimera

The tutorial will guide you through the step-by-step procedure to dock a small molecule ligand amino acid (L-Asp) to a protein receptor (AspRS) by using AutoDock Vina integrated with Chimera. Model system: Aspartyl-tRNA-synthetase.

[@tagscientist]

Having laboured through 3 other YT tutorials on this exact same topic, I can say this is far and away the best tutorial. I am left wondering if the other presenters actually knew what they were talking about. This tutorial is authoritative, straightforward and well presented - excellent stuff. Thank you.

[@zishuocheng3682]

It is informative and very easy to follow. Thanks

[@BharathKumar-mu1dy]

Very well explained sir.

[@DrSam-qe1sk]

Very informative lecture.

[@professorswenson3504]

How do you know what net charge to add to the ligand during preparation? Should it always be 0? For example, I have downloaded ATP from PubChem. It has several deprotonated phosphate groups, do I need to specify in Chimera the negative3 charge? Thank you!

[@sikhaborah5090]

Sir why I can't paste the smiles from pubchem to ucsf chimera

[@ikponwmosaobaseki3645]

nice

[@hanstsahnang4533]

Thanks very much for this tutorial professor. Please Sir after doing redocking, if your ligand aligns with the cocrystallised ligand but doesn't have a good RMSd value which parameters can you modify to have a perfect alignment which will lead to a good RMSd value? Thanks

[@hanstsahnang4533]

thanks for this tutorial. can tell how to calculate RMSD value of redocked complex ? if when calculating rmsd value you get a value lower than 1 say 0.235 is it bad for a docking experiment?

[@ajagunebelejoan3164]

Thank you. Please how can I get my binding site for command prompt

[@suyashsawale9508]

There is an error shown - [Error 13] permission denied: complex.pdbqt. How to rectify???

[@sarika1122]

How download auto dock vina.last step auto dock does no work.for window 10

[@vernonvest5104]

hello sir, I am using MacBook Air M1 which MGL tools is not available, can I use UCSF chimera as an alternative for MGL tools?

[@amandalaseke7523]

I am also struggling to do docking with a Mac

[@ItsSAAL]

I love you

[@GODislove777trustGOD]

actual docking: 10:37