Week1 Jan17 Jan21 - WangXueqing007/Master_Thesis GitHub Wiki

Jan 17:

  • First meeting for my project!
  • Today: Finishing installing AutoDock, AutoDock Vina and ADT (plus XQuartz). Rearranged my folders on PC (i.e. Downloads) and google drive. Started to read AutoDock tutorial and organized the first-stage plan. Cheers!
  • According to Sarah:
    • All the functions in AutoDock command line can be found in the user interface. so start from the user interface.
    • AutoDock can calculate (predict) all the possible binding sites in the given receptor (protein) and these pockets can be visualized in ADT. ADT can also cluster these pockets (so they won't be shown in a mess). The usual way to do it is to download the file and visualize it in VMD instead.
    • "High-throughput"?
  • To do: Background knowledge about insecticides and pLGICs! And learn to use Endnote! !

Problem: Spent a lot of time on the switching among directories! Can this be solved?

Jan 18:

  • Follow the ADT tutorial, get to exercise 8 (haven't launched). Started to get on line with ADT.
  • To do: Read about 20 amino acids! !

Thoughts in mind:

  • For the introduction part in thesis:
    1. Don't start from others' structure. Build your own structure and look into others' for any missing points.
    2. Start right away! Write then you read!

Jan 19:

  • Meeting:
    • Ligand-isometrics
    • Receptor-need to try several simulation frames
  • Today:
    • Two group meetings.
    • For AutoDock (PMV): Get stuck with the "depth-first-order" traversal bug (ERROR: All ATOM and HETATM records must be given before any nested BRANCHes; see line ## in PDBQT file "xxx.pdbqt"). Found similar problem description on Internet but not solution. Took quite a while...
      Haven't been solved!
    • For ligand conformation searching: SMILE website failed. But managed to found the structure of lindane, fipronil and ivermectin on Pubchem Literture: Finished Tanja's report.

Jan 20:

  • Today:

    Little done. Had my Saturday!
    Read Stephanie's pharmaceutical paper (haven't fully finished)

  • Communication (through either oral or writing) in science is super important!
  • To do: Terminologies of compounds and functional groups!