Week 3 Jan 29 Feb 4 - WangXueqing007/Master_Thesis GitHub Wiki
Jan 29:
I want to develop a solid pipeline for defining grids and turn the channel into an appropriate coordinate--is that doable?
I don't feel like that turning the coordinate is a good idea...It is not easy to visualize in 3D space, and the angle is not accurate. I would rather adjust the grid instead...
Jan 30:
Today: Docked lindane to the pore area of one isoform in 4npq. In 4 folders.
Repeat three times in AutoDock manually.
Have to figure out how t do "high-throughput" in bash.
Learn more about coordinate adjusting in VMD.
Will do: docking of PFL to 5MUO.
More notes on notebook.
Jan 31:
PFL-5MUO result: doesn't bind to the position in co-crystallization structure.
Dec 2:
GLIC Meeting:
Sarah: Docking is perhaps better for checking the difference among different compounds than finding different binding positions of one compound?
The contradictory results: could be that PFL and lindane are not very specific bound in GLIC? PFL rather binds in the subunits?
To do: build up the statistics; look into fipronil?
Fipronil: on one hand more specific binding; on the other hand limited (?)
Clustering?
What I did today:
Two meetings.
Tried VMD VolMap Tool--> choose "pdb" as input file type.
Read a bit into the third tutorial.
Figured out the clustering.sh script, tried to download GROMACS...
To-do list!
Linux basic--shell script...
Figuring out a good way to present the docking results: Ideally, by next Friday, docking results of PFL, lindane, fipronil, to two structures (perhaps 20x20?).