# COVID-19 Project

[](https://hackmd.io/W81hymKPTK2Pzn2qk5JJJg)

## Analysis
All analysis are in Jupyter notebook files.
Root path: `./Analysis/`
`Gromacs_RMSF.ipynb`: RMSF analysis file.
`Gromacs_data_wTIME.ipynb`: root mean squre deviation (RMSD)/Radius of gyration (Rg)/Number of hydrogen bonds and pairs(HB-pairs)/correlation between hydrogen bonds and pairs (corr-HB) over time.
`Gromacs_distribution.ipynb`: distribution of distance and angle of hydrogen bonds.
`Gromacs_equilibrium.ipynb`: energy/temperature/pressure/density in equilibrium process (energy minimization/NVT/NPT).
`Gromacs_features_clustering.ipynb`: using molecular dynamics features for clustering into different variants.
`Gromacs_hbac_fitting.ipynb`: analaysis of autocorrelation of hydrogen bonds (fitting, calculating relaxation time of hydrogen bonds, and so on).
`VariantsFreqVaccPlot.ipynb`: integrate multiple sources public health data (proportion of vaccinated individuals/variant frequency) into single plot.

## Data
Data for analysis (from public health resources or molecular dynamics).
Root path: `./Data/`

### gromacs parameter files
Path: `./Data/gromacs_mdp`
`ions.mdp`: parameter file when adding ions.
`md.mdp`: parameter file when performing molecular dynamics for 100 ns.
`minim.mdp`: parameter file when performing energy minimization (EM).
`npt.mdp`: parameter file when perfomring equilibrium in normal pressure temperature (NPT).
`nvt.mdp`: parameter file when perfomring equilibrium in normal volume temperature (NVT).

### metadata
Path: `./Data/metadata`
`CoVariants_data`: public health data from CoVariants (about variant frequency).
`Owid_data`: public health data from Our World in Data (about proportion of vaccinated individuals).
`md_tidydata`: tidy data of molecular dynamics data.
* `ComparisonOfVariants.xlsx`: All tidy data here.
* `ComparisonOfVariants_numeric.csv`: Numeric tidy data for further analysis (e.g. clustering).
* `ComparisonOfVariants_wMutual_numeric.csv`: Numeric tidy data for further analysis (e.g. clustering). Mutual residues among different PDB model were selected in analysis of RMSD/Rg so that the deviation from different PDB can be reduced.
* `RMSF.csv`: RMSF data for following analysis.

### raw data
Path: `./Data/rawdata`

#### Molecular dyanmics (MD) results
`variants_6m0j`: WT/alpha/beta/gamma/delta/delta plus/epsilon/gamma/lambda/mu/omicron.
`variants_7a91`: WT/alpha/beta/gamma/delta/delta plus/epsilon/gamma/lambda/mu/omicron.
`variants_7mjn`: alpha.
`variants_7v80`: beta.
`variants_7v84`: gamma.
`variants_7v8b`: delta.

***Each folder contains the following items:***
* `6m0j_WT_afterMD_dimplot`: Ligplot+ dimplot with chord plot by python3 script [here](https://github.com/yuyuan871111/dimpyplot_chordplot) (with after MD structure).
* `6m0j_WT_beforeMD_dimplot`: Ligplot+ dimplot with chord plot by python3 script [here](https://github.com/yuyuan871111/dimpyplot_chordplot) (with before MD structure).
* `2dproj.xvg`: PCA analysis for trajectory.
* `6m0j_WT_afterMD.pdb`: initial structure before MD.
* `6m0j_WT_beforeMD.pdb`: final structure after MD.
* `density_npt.xvg`: denesity over time in NPT.
* `gyrate.xvg`: Rg over time.
* `gyrate_mutual.xvg`: Rg over time with mutual residues among 6m0j, 7a91, 7mjn, 7v80, 7v84, 7v8b.
* `hbac.xvg`: autocorrelation of hydrogen bonds between hACE2 and S1RBD.
* `hbang.xvg`: distribution of the angle of hydrogen bonds.
* `hbdist.xvg`: distribution of the distance of hydrogen bonds.
* `hbnum.xvg`: number of hydrogen bonds and pairs over time.
* `md_protein.xtc`: compressed trajectory of 100 ns MD.
* `potential_em.xvg`: energy over time in EM.
* `pressure_npt.xvg`: pressure over time in NPT.
* `rmsd.xvg`: RMSD over time.
* `rmsd_mutual.xvg`: RMSD over time with mutual residues among 6m0j, 7a91, 7mjn, 7v80, 7v84, 7v8b.
* `rmsf_S1RBD.xvg`: RMSF in S1RBD regions.
* `rmsf_hACE2.xvg`: RMSF in hACE2 regions.
* `temperature_nvt.xvg`: temperature over time in NVT.

#### pdb input
All pdb input for whole molecular dynamics procedure were backuped in `./Data/rawdata/pdb_input`.

## Structural Analysis Tools
A python 3 self-defined packaged for this study, which might be used in analysis.
Root path: `./StructuralAnalysisTools`

## Visualization
Figures were generated from analysis including graphical abstract, structrual view, MD results over time, fitting curves, ...
Root path: `./Visualization/`
### illustration
* `illu/COVID_variants_v*.png`: mutations information in different PDBs (* is the version number).
* `illu/MyCOVID_Project_Workflow_v*.png`: graphical abstract of my analysis (* is the version number).
### other plots
* `DimChordplot`: chord plot before and after MD in different PDB models/in different variants.
* `MD`: molecular dyanmics results.
AngleDistribution.png / CorrBetweHBandContac.png / DistDistribution_focus.png / DistDistribution_raw.png / Equilibrium_6m0j.png / Equilibrium_7a91.png / Equilibrium_groundtrue.png / HBautocorr.png / HBnum.png / HBnum35.png / RMSD.png / RMSD_mutual.png / RMSF.png / RadiusOfGyration.png / RadiusOfGyration_mutual.png
* `MDfeatures_clustering`: attempt to cluster into variants with MD features by different methods.
* `Omicron`: omicron results including MD results/Clustering map/structural view.
* `PublishData`: data for publication.
`Corre_clustering.png`: correlation of MD features and variants clustering map ***without*** data selecting mutual residues in RMSD/Rg analysis.
`Corre_clustering_wMutual_*.png`: correlation of MD features and variants clustering map ***with*** data selecting mutual residues in RMSD/Rg analysis (* is the version number).
`DistDistribution_all.png`: distribution of distances of hydrogen bonds (overall/focus on certain range) without omicron result.
`HBnum_all.png`: the number of hydrogen bonds over time (6m0j/7a91/ground truth) without omicron result.
`RMSD_Rg_HBac.png`: results of RMSD/Rg/autocorrelation of hydrogen bonds ***without*** data selecting mutual residues in RMSD/Rg analysis.
`RMSD_Rg_HBac_mutual.png`: results of RMSD/Rg/autocorrelation of hydrogen bonds ***with*** data selecting mutual residues in RMSD/Rg analysis.
`Reuters_graphics_20211123_anno.png`: public heatlh plots from Reuters with manual annotation of variant shifts.
`VariantVaccPlot_freq_****_anno.png`: variant frequency plots (with public health data from CoVariants and Our World in Data) with manual annotation of variant shifts (**** is the date of plotting).
`VariantVaccPlot_freq_1228_anno_filterBias.png`: variant frequency plots (with public health data from CoVariants and Our World in Data) with manual annotation of variant shifts (**** is the date of plotting); filtering the bias in Israel case.
`delta_structural_chord_v*.png: structural view and chord plot for the results of the delta variant (* is the version number).
* `Reuters`: raw public heatlh plots from Reuters.
* `StructuralView`: raw data of strucutral views of the results of the delta variant.
* `VariantFrequency`: raw variant frequency plots with public health data from CoVariants and Our World in Data.

## Variants in this study
| WHO label | PANGO lineage | PDB |
| -------- | -------- | ----- |
| Wild type | - | 6m0j, 7a91 |
| Omicron | BA.1 | 6m0j+schrodinger, 7a91+schrodinger |
| Omicron | BA.2 | 6m0j+schrodinger, 7a91+schrodinger |
| Omicron | BA.2.12.1 | 6m0j+schrodinger, 7a91+schrodinger |
| Omicron | BA.4&5 | 6m0j+schrodinger, 7a91+schrodinger |
| Alpha | B.1.1.7 | 6m0j+schrodinger, 7a91+schrodinger, 7mjn |
| Beta | B.1.351 | 6m0j+schrodinger, 7a91+schrodinger, 7v80 |
| Gamma | P.1 | 6m0j+schrodinger, 7a91+schrodinger, 7v84 |
| Delta | B.1.617.2 | 6m0j+schrodinger, 7a91+schrodinger, 7v8b |
| Delta Plus | AY.1 | 6m0j+schrodinger, 7a91+schrodinger |
| Epsilon | B.1.427/9 | 6m0j+schrodinger, 7a91+schrodinger |
| Lambda | C.37 | 6m0j+schrodinger, 7a91+schrodinger |
| Mu | B.1.621 | 6m0j+schrodinger, 7a91+schrodinger |
| Mu -R346K | - | 6m0j+schrodinger, 7a91+schrodinger |
* 6m0j: `S1RBD:333-526; hACE2:19-615`
* 7a91: `S1RBD:323-555; hACE2:19-133,141-613`
* 7mjn, 7v80, 7v84, 7v8b: `S1RBD:331-530; hACE2:19-614`

### Mutation list in region of interst (S1RBD: 323-555)

## Resources
* [WIKI: variants of SARS-COVID-2](https://en.wikipedia.org/wiki/Variants_of_SARS-CoV-2)
* Websites
* [Nextstrain](https://nextstrain.org/groups/neherlab/ncov)
* [CoVariants](https://covariants.org/)
* [Reuters COVID tracker](https://graphics.reuters.com/world-coronavirus-tracker-and-maps/)
* Database
* [Covid variant visualization (COVDB)](https://covdb.stanford.edu/)
* [SCoV2-MD](https://submission.gpcrmd.org/covid19/home/)
* [VarEPS](https://nmdc.cn/ncovn/)
* [COVID19db](http://www.biomedical-web.com/covid19db/home)
* [Ensembl for Covid-19](https://covid-19.ensembl.org/index.html)
* [SCovid](http://bio-annotation.cn/scovid/#/)
* [T-CoV](https://t-cov.hse.ru/)
* Articles related to this study [[link](./Related_references.md)]