How to analysis the Autodock Vina results by UCSF Chimera?

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  • เผยแพร่เมื่อ 23 ธ.ค. 2024

ความคิดเห็น • 11

  • @sudheshnabodapati172
    @sudheshnabodapati172 3 ปีที่แล้ว

    This was great, thank you! I hope you can help me with the below questions
    How do we analyze and find mutations and conformational changes in the protein because of those mutations and also if the mutations affect the protein-ligand interactions?
    How do we find out which binding sites have sites more affinity than the other?

    • @al1r3z49
      @al1r3z49  3 ปีที่แล้ว +1

      Hello. Thank you so much for seeing the video. The simplest way to see a conformational change due to amino acid substitution is 'structural alignment' of the mutant protein to the wild type. You can always benefit of Uniprot.org to find out known mutations of a certain protein. If you wanna know amino acid substitution change the affinity of a ligand to the protein I suggest this video: th-cam.com/video/W1VG4c_5umk/w-d-xo.html.
      For your last question, to my knowledge, molecular docking is not the way for assessing a single amino acid affinity to a ligand or vice verse. This requires molecular dynamic simulation. I wish you best.

  • @tarotwithstarrs777
    @tarotwithstarrs777 2 ปีที่แล้ว +1

    How to manually highlight interactive residues? Everytime I try to label, it labels every redidue

    • @al1r3z49
      @al1r3z49  2 ปีที่แล้ว

      Dear Monika, if you want to manually highlight some certain residues do as follow:
      1. Select a chain (optional)
      2. From toolbar go to Favorits---> Sequence
      3. Hold Ctrl and select residues in a chain
      4. Go to Action and modify the selected residues.
      I hope you have fun editing. 👌

  • @MinaYari-vr2bn
    @MinaYari-vr2bn 7 หลายเดือนก่อน

    Your video is really useful, thanks 🙏🙏

    • @al1r3z49
      @al1r3z49  7 หลายเดือนก่อน

      Thanks for watching

  • @skobichevskii
    @skobichevskii 3 หลายเดือนก่อน

    how can i find out the binding energy?

    • @al1r3z49
      @al1r3z49  3 หลายเดือนก่อน

      Dear sir, the binding energy is an output of the docking results. For example, you can see the binding free energy after docking with Autodock. In this video, I have only show how to present or visualize the docking, meaning how the ligand is attached or posed in its biding site within the receptor.

  • @sarigueya
    @sarigueya 2 ปีที่แล้ว

    thank you for the video!!!

    • @al1r3z49
      @al1r3z49  2 ปีที่แล้ว

      @Juan thank you for watching.

  • @cpfgroup9416
    @cpfgroup9416 2 ปีที่แล้ว +1

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