[CHODERA LAB] Literature and structure review planning

FoldingAtHome / coronavirus

Folding@home COVID-19 efforts

https://foldingathome.org

1.09k stars 80 forks source link

[CHODERA LAB] Literature and structure review planning #24

Open rafwiewiora opened 4 years ago

rafwiewiora commented 4 years ago

@zhang-ivy @apayne97 @jiayeguo @egoldber @hannahbrucemacdonald @jchodera

We're going to work out here who's doing what and how they'll organize it.

rafwiewiora commented 4 years ago

@Henriberger

egoldber commented 4 years ago

Okay I am going to work on...

team up with @jiayeguo to work on the mermaid flow diagram/timeline of the stages of infection for both SARS and SARS-2
work through literature. Idea to not step on each others toes: I am going to update the current "README.md" with a list of the current zotero articles. I'll make it a table of "article name" and then a second column with "Dibbs" and you guys can go in and edit as you want? Or we can make it a seperate .md file?

apayne97 commented 4 years ago

I will work on adding papers to our list to read, update the "dibbs" chart to reflect what I'm going to read, and help write the descriptions and collect the information for the mermaid diagram.

zhang-ivy commented 4 years ago

Outline for directory structure:

coronavirus
- system_preparation
- literature
  - README will contain table of each paper along with a short (2 sentence ish) summary
  - sub-directories for each paper
    - each README will contain the annotated bibliography of the paper
- target-info
  - README will contain diagram showing different stages of SARS vs. SARS-2 (although I would assume that everything we know about SARS-2 right now is based on SARS)
  - directory for each target containing key papers.
    - each README will contain background, pdb ids, existing drugs, preparation notes, hypotheses (not necessarily in this order)

Erica has already created an add-literature branch, we should also create a add-target-info branch

jiayeguo commented 4 years ago

I am going to work on:

[ ] together with @egoldber and @apayne97 to work on the mermaid flowchart of covid19 infection stages compared with SARS (which proteins are involved in each stage and what are their vulnerability as drug targets);
[ ] General reading on those proteins and place the currently available structures (and other info) listed in Erica’s google doc file into the flowchart.