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