Protein-ligand docking with AutoDock Vina and UCSF Chimera

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  • Опубліковано 9 січ 2025

КОМЕНТАРІ • 21

  • @tagscientist
    @tagscientist Рік тому +1

    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.

  • @ingshang7138
    @ingshang7138 2 дні тому

    Great guideline! Thanks a lot😊

  • @zishuocheng3682
    @zishuocheng3682 3 роки тому +2

    It is informative and very easy to follow. Thanks

  • @BharathKumar-mu1dy
    @BharathKumar-mu1dy 3 роки тому +1

    Very well explained sir.

  • @DrSam-qe1sk
    @DrSam-qe1sk 2 роки тому +1

    Very informative lecture.

  • @IshitaSahu-e2l
    @IshitaSahu-e2l Місяць тому

    We can clear the work by clicking on file then close session instead of closing the software.

  • @hanstsahnang4533
    @hanstsahnang4533 2 роки тому

    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

  • @professorswenson3504
    @professorswenson3504 7 місяців тому

    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!

  • @NimraAsghar-kv2go
    @NimraAsghar-kv2go 3 місяці тому

    in my case command line residues are not showing and also binding pockets are not showing the residues.. what should I do?

  • @vanderburg.M
    @vanderburg.M 17 днів тому

    VERY GOOD

  • @ajagunebelejoan3164
    @ajagunebelejoan3164 2 роки тому

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

  • @hanstsahnang4533
    @hanstsahnang4533 3 роки тому

    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?

  • @GODislove777trustGOD
    @GODislove777trustGOD 2 роки тому

    actual docking: 10:37

  • @sikhaborah5090
    @sikhaborah5090 8 місяців тому

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

  • @vernonvest5104
    @vernonvest5104 3 роки тому

    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
      @amandalaseke7523 3 роки тому +2

      I am also struggling to do docking with a Mac

  • @suyashsawale9508
    @suyashsawale9508 2 роки тому

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

  • @Ramaa_taless
    @Ramaa_taless Місяць тому

    I need help in docking

  • @sarika1122
    @sarika1122 2 роки тому

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

  • @ikponwmosaobaseki3645
    @ikponwmosaobaseki3645 3 роки тому +1

    nice

  • @ItsSAAL
    @ItsSAAL 10 місяців тому

    I love you