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# Forkwell Coronavirus Hack: Drug Discovery
[Fork](https://guides.github.com/activities/forking/) this repository to start participating!
[](https://discord.gg/jFjbXqp)
## About
Welcome to [Forkwell Coronavirus Hack](https://www.forkwell.io/events/forkwell-coronavirus-hack)!
This repository contains the hackathon kit for you to get started on solving **topic 1: Drug
Discovery** and eventually a place where you host all your submission artifacts as your own fork.
## Sponsors
| [](https://microsoft.com/) | [](https://mdec.my/) | [](https://runcloud.io/) |
|--------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------|
| [](https://aws.amazon.com/) | [](https://do.co/forkwell) | [](https://innovationlabs.sunway.edu.my/) |
| [](https://www.coronatracker.com) | [](https://www.thelead.io/) | [](https://aigeeks.net/) |
## Background
A few studies have shown that HIV antivirals offer promising results, but this is still an open
field of discovery.
Finding a new drug or validating an existing drug are both suitable approaches.
## Goal
Find a candidate drug (ligand) with a high binding affinity with the COVID-19 main protease.
1. Use machine learning to identify a potential candidate, then use docking software to get the
binding affinity between it and the main protease.
2. Write a report that describes your process and results in detail in the form of a jupyter
notebook.
## Submission
You are required to submit a 15-minute presentation video of your report. However, to ensure the
legitimacy of your submission, you are required to submit your project artifacts (code, datasets,
documents) as a [fork](https://guides.github.com/activities/forking/) to this repository.
A submission form will be available on the 14th of April 2020 for submission,
please join our
[facebook](https://facebook.com/groups/forkwellcoronavirushack/) group and
[discord](https://discord.gg/jFjbXqp) channel to keep updated with latest changes.
After creating your own [fork](https://guides.github.com/activities/forking/)
of this repository, clone the repository:
```sh
git clone [email protected]:<your-github-username>/fch-drug-discovery
```
Change to the directory:
```sh
cd fch-drug-discovery
```
Set upstream:
```sh
git remote add upstream [email protected]:forkwell-io/fch-drug-discovery
```
...and start Hacking!!
Once you are ready to submit, create a pull request from your
[fork](https://guides.github.com/activities/forking/) to us and include the link to your fork in
your submission form that will be available on the 14th of April 2020.
Please remember that your code will be publicly available, open-sourced licesed and free for the
internet to use. Please ensure that you don't commit any sensitive information!
## Resources
### Presentations
[](https://drive.google.com/open?id=1pHy9Cm4_w4Ri8lVbcN2XC637_7BaLL9P)
*Virus Primer - Target a Virus*
**Thomas MacDougall - Graduate Student in Computer Science at the University of Montreal**
*[slides](https://drive.google.com/drive/folders/1YsyUQQBAIxq_syXzE6wxSPaifAwmNxxF)*
---
### Databases
| Name | Link |
|-----------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------|
| CMap | https://clue.io/cmap |
| COVID-19 main protease | https://www.wwpdb.org/pdb?id=pdb_00006lu7 |
| ChemBL | https://www.ebi.ac.uk/chembl/ |
| DrugBank | https://www.drugbank.ca/ |
| Folding@Home | https://github.com/FoldingAtHome/coronavirus |
| Formatted ZINC Database | https://github.com/molecularsets/moses |
| GEO Signatures of Differentially Expressed Genes for Viral Infections | https://amp.pharm.mssm.edu/Harmonizome/dataset/GEO+Signatures+of+Differentially+Expressed+Genes+for+Viral+Infections |
| NextStrain | https://nextstrain.org/ |
| ZINC Database | https://zinc.docking.org/ |
| Dataset Search | https://blog-google.cdn.ampproject.org/c/s/blog.google/products/search/discovering-millions-datasets-web/amp/ |
### APIs
| Name | Link |
|----------------------|---------------------------------------------------------------------------------------------------------|
| CoronaTracker API | https://api.coronatracker.com |
| COVID-19 Postman API | https://covid-19-apis.postman.com/ |
| COVID-19 Rapid API | https://rapidapi.com/api-sports/api/covid-193?endpoint=apiendpoint_dfb9e52d-bd90-48ec-a571-8b78610a736d |
### Docking Tools
| Name | Link |
|-----------------------|---------------------------------------------------|
| AutoDock VINA | http://vina.scripps.edu/ |
| PyRX | https://pyrx.sourceforge.io/ |
### Deep Reinforcement Learning Networks
| Name | Link |
|---------|--------------------------------------------|
| DrugEx | https://github.com/XuhanLiu/DrugEx |
| GENTRL | https://github.com/insilicomedicine/GENTRL |
| ReLeaSE | https://github.com/isayev/ReLeaSE |
## Awesome perks from our sponsors!
Deployment
- [DigitalOcean](https://do.co/forkwell)
E-learning
- [Microsoft Learn](https://aka.ms/learn)
## Help us organize better
Feel free to open issues if you find anything lacking and we appreciate your feedback greatly!
## Community
Join the community!
- [Discord](https://discord.gg/jFjbXqp)
- [Forkwell Facebook Group](https://facebook.com/groups/forkwellcoronavirushack/)