Difference between revisions of "Progress:Kevin"

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(20160817)
(20160817)
Line 11: Line 11:
 
#* martini
 
#* martini
 
# <span style="color: red">PIP2/PS Umbrella sampling
 
# <span style="color: red">PIP2/PS Umbrella sampling
#* 1-PIP2, 2-PC
+
#* <span style="color: LightGrey">1-PIP2, 2-PC
 
#* 1-PC, 2-PIP2
 
#* 1-PC, 2-PIP2
 
#* 1-PS, 2-PC
 
#* 1-PS, 2-PC

Revision as of 15:27, 17 August 2016

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

Checked
To be discussed
In progress

20160817

  1. Actin analysis
  2. Peptide setup
    • All-atom
    • martini
  3. PIP2/PS Umbrella sampling
    • 1-PIP2, 2-PC
    • 1-PC, 2-PIP2
    • 1-PS, 2-PC

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
  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