Difference between revisions of "Progress:Kevin"
From Computational Biophysics and Materials Science Group
| 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 /> | ||
| + | |||
| + | =20161115= | ||
| + | # <span style="color: red">manuscript MDFF | ||
| + | #* Comments from | ||
| + | #** Lu | ||
| + | #*** Soft words on asymmetrical dynamics | ||
| + | #*** Add some PTMC results | ||
| + | #*** Mute/Clerify Class 2 results | ||
| + | #*** Remove energy tables | ||
| + | #*** RMSF analysis of asymmetrical simulations | ||
| + | #*** Compare structure at different states | ||
| + | #** Sun | ||
| + | #** Xiaoyun | ||
| + | #** Zhou | ||
| + | # <span style="color: red">manuscript Ups | ||
| + | #* PCA study of Ups | ||
| + | #* Reply Yu-jia | ||
=20160921= | =20160921= | ||
| − | # <span style="color: | + | # <span style="color: lightgrey">Extend |
#* Ups1 | #* Ups1 | ||
#* Asymmetrical 2 | #* Asymmetrical 2 | ||
| Line 15: | Line 32: | ||
#* PH rotational angles | #* PH rotational angles | ||
#* Introduction | #* Introduction | ||
| − | # <span style="color: | + | # <span style="color: lightgrey">MDFF manuscript figures |
#* move PTMC to supp | #* move PTMC to supp | ||
#* tetramer simulations | #* tetramer simulations | ||
Revision as of 20:53, 15 November 2016
This page is used for checklists discussed during the weekly meetings.
Checked
To be discussed
In progress
Contents
[hide]20161115
- manuscript MDFF
- Comments from
- Lu
- Soft words on asymmetrical dynamics
- Add some PTMC results
- Mute/Clerify Class 2 results
- Remove energy tables
- RMSF analysis of asymmetrical simulations
- Compare structure at different states
- Sun
- Xiaoyun
- Zhou
- Lu
- Comments from
- manuscript Ups
- PCA study of Ups
- Reply Yu-jia
20160921
- Extend
- Ups1
- Asymmetrical 2
20160831
- JPCB manuscript
- US results
- PH rotational angles
- Introduction
- MDFF manuscript figures
- move PTMC to supp
- tetramer simulations
- RMSF profiles
20160817
- PIP2/PS Umbrella sampling submit
- 1-PIP2, 2-PC
- 1-PC, 2-PIP2
- 1-PS, 2-PC
- Peptide setup
- All-atom
- martini
- Actin analysis
20160727
- US of BN-lipids
- help Yonghui setting up US in Gromacs, 2 set-ups (BN and membrane), DMPC, 3 temperatures
- Ups figure
- COM between protein and lipids
- tilting angles
- distance between residues (<10) and DOPA (resid 257)
- vector of binding pocket with membrane
- Next BAR-PH paper
- Theme: lipid specificity
- contacting residues in BAR-PH--membrane MD
- Setup US of PIP2/PS with PH domain
- Martini
- many constrained BAR-PH on membrane
- Actin
- new MD data
- Others
- Send cluster configurations to CSC
- Move mini
- Quotation for new storage disks
20160720
- Ups figure
- read manuscript
- examine contacting residues
- discuss
- Next BAR-PH paper
- examine contacting residues
- discuss
20160713
- Summarize BAR-PH simulations
- Sun: compare stability of tetramers
- Sun: to be discussed for the manuscript
- Prepare Ups figures
20160706
- 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
- Figure indexes
- revised
- Figure “rotational PH” revised
- split into main and supp
- re-plot distribution and delete class 2
- re-draw schematic
- add bin size
- Figure "assembly process" revised
- revised and polished
- move legends
- Figure “structural angle”
- re-plot to distribution
- 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
- Check residues
- Text name of interfaces: same-row, different-row, front, back interactions
