Difference between revisions of "Progress:Kevin"

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Line 4: Line 4:
 
To be discussed<br />
 
To be discussed<br />
 
<span style="color: red">In progress<br />
 
<span style="color: red">In progress<br />
 +
 +
=20160727=
 +
# <span style="color: red">US of BN-lipids
 +
#* help Yonghui setting up US in Gromacs, 2 set-ups (BN and membrane), DMPC, 3 temperatures
 +
# <span style="color: ">Ups figure
 +
#* <span style="color: red">COM between protein and lipids
 +
#* <span style="color: red">tilting angles
 +
#* <span style="color: red">distance between residues (<10) and DOPA (resid 257)
 +
#* <span style="color: red">vector of binding pocket with membrane
 +
# Next BAR-PH paper
 +
#* Theme: lipid specificity
 +
#* <span style="color: red">contacting residues in BAR-PH--membrane MD
 +
#* <span style="color: red">Setup US of PIP2/PS with PH domain
 +
#* <span style="color: red">read James' paper
 +
# Martini
 +
#* <span style="color: red">many constrained BAR-PH on membrane
 +
# Actin
 +
#* <span style="color: red">new MD data
 +
# Others
 +
#* <span style="color: red">Send cluster configurations to CSC
 +
#* <span style="color: red">Move mini
 +
#* <span style="color: red">Quotation for new storage disks
 +
 +
=20160720=
 +
# <span style="color: LightGrey">Ups figure
 +
#* read manuscript
 +
#* examine contacting residues
 +
#* discuss
 +
# <span style="color: LightGrey">Next BAR-PH paper
 +
#* examine contacting residues
 +
#* discuss
 +
 +
=20160713=
 +
# <span style="color: red">Summarize BAR-PH simulations
 +
#* Sun: compare stability of tetramers
 +
#* Sun: to be discussed for the manuscript
 +
# <span style="color: LightGrey">Prepare Ups figures
  
 
=20160706=
 
=20160706=
Line 30: Line 67:
 
# <span style="color: LightGrey">Check residues
 
# <span style="color: LightGrey">Check residues
 
# <span style="color: LightGrey">Text name of interfaces: same-row, different-row, front, back interactions
 
# <span style="color: LightGrey">Text name of interfaces: same-row, different-row, front, back interactions
−
 
−
=20160713=
 
−
# <span style="color: red">Summarize BAR-PH simulations
 
−
#* Sun: compare stability of tetramers
 
−
#* Sun: to be discussed for the manuscript
 
−
# <span style="color: LightGrey">Prepare Ups figures
 
−
 
−
=20160720=
 
−
# <span style="color: LightGrey">Ups figure
 
−
#* read manuscript
 
−
#* examine contacting residues
 
−
#* discuss
 
−
# <span style="color: LightGrey">Next BAR-PH paper
 
−
#* examine contacting residues
 
−
#* discuss
 
−
 
−
=20160727=
 
−
# <span style="color: red">US of BN-lipids
 
−
#* help Yonghui setting up US in Gromacs, 2 set-ups (BN and membrane), DMPC, 3 temperatures
 
−
# <span style="color: ">Ups figure
 
−
#* <span style="color: red">COM between protein and lipids
 
−
#* <span style="color: red">tilting angles
 
−
#* <span style="color: red">distance between residues (<10) and DOPA (resid 257)
 
−
#* <span style="color: red">vector of binding pocket with membrane
 
−
# Next BAR-PH paper
 
−
#* Theme: lipid specificity
 
−
#* <span style="color: red">contacting residues in BAR-PH--membrane MD
 
−
#* <span style="color: red">Setup US of PIP2/PS with PH domain
 
−
#* <span style="color: red">read James' paper
 
−
# Martini
 
−
#* <span style="color: red">many constrained BAR-PH on membrane
 
−
# Actin
 
−
#* <span style="color: red">new MD data
 
−
# Others
 
−
#* <span style="color: red">Send cluster configurations to CSC
 
−
#* <span style="color: red">Move mini
 
−
#* <span style="color: red">Quotation for new storage disks
 

Revision as of 18:11, 20 July 2016

This page is used for checklists discussed during the weekly meetings.

Checked
To be discussed
In progress

20160727

  1. US of BN-lipids
    • help Yonghui setting up US in Gromacs, 2 set-ups (BN and membrane), DMPC, 3 temperatures
  2. Ups figure
    • COM between protein and lipids
    • tilting angles
    • distance between residues (<10) and DOPA (resid 257)
    • vector of binding pocket with membrane
  3. Next BAR-PH paper
    • Theme: lipid specificity
    • contacting residues in BAR-PH--membrane MD
    • Setup US of PIP2/PS with PH domain
    • read James' paper
  4. Martini
    • many constrained BAR-PH on membrane
  5. Actin
    • new MD data
  6. Others
    • Send cluster configurations to CSC
    • Move mini
    • Quotation for new storage disks

20160720

  1. Ups figure
    • read manuscript
    • examine contacting residues
    • discuss
  2. Next BAR-PH paper
    • examine contacting residues
    • discuss

20160713

  1. Summarize BAR-PH simulations
    • Sun: compare stability of tetramers
    • Sun: to be discussed for the manuscript
  2. Prepare Ups figures

20160706

  1. Revision on supplementary text and legends
    • colour definitions added to legends
    • comparison between before and after MDFF added
    • comparison between MDFF and rigid-body docking added
  2. Figure indexes
    • revised
  3. Figure “rotational PH” revised
    • split into main and supp
    • re-plot distribution and delete class 2
    • re-draw schematic
    • add bin size
  4. Figure "assembly process" revised
    • revised and polished
    • move legends
  5. Figure “structural angle”
    • re-plot to distribution
  6. PTMC
    • PTMC of BAR-PH added to Fig1
    • PTMC of other BAR added to Supp
    • tables modified
    • add two supp figures
    • add supp text on other BARs
  7. Check residues
  8. Text name of interfaces: same-row, different-row, front, back interactions

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