COVID-19 Genomic Sequence Ideas

Pseudo Use Cases

NextStrain

Real-time tracking of pathogen evolution
Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. We provide a continually-updated view of publicly available data alongside powerful analytic and visualization tools for use by the community. Our goal is to aid epidemiological understanding and improve outbreak response.

GenData2
DATA: https://github.com/nextstrain/ncov/blob/master/data/metadata.tsv
JSON API: http://data.nextstrain.org/ncov.json

Brute Force COVID-19 Evolution

Based on a 2018 chemistry Nobel Prize https://www.chemistryworld.com/news/what-is-directed-evolution-and-why-did-it-win-the-chemistry-nobel-prize/3009584.article The thought is to brute force all possible evolutions of COVID-19 to create inhibitors that would block the negative side effects cause by COVID-19.
http://www.rcsb.org/pdb/results/results.do?tabtoshow=Current&qrid=76FE267D

Find Current Drug to Effectively Treat COVID-19

Take a look at current drugs and which ones would be more effective in treating COVID-19. Look at Harmonizome (72 million functional associations between genes and attributes?

Possible Steps:

  1. Collect data
  2. include connective weights
  3. find how different molecules are related based on their total biomarker connectivity
    https://deepmind.com/blog/article/AlphaFold-Using-AI-for-scientific-discovery

CMap

The CMap dataset of cellular signatures catalogs transcriptional responses of human cells to chemical and genetic perturbation. Here you can find the 1.3M L1000 profiles and the tools for their analysis.
https://clue.io/data/

Genome Similarity

Whole Genome

Whole genome of coronaviruses
https://webs.iiitd.edu.in/raghava/coronavir/genome.php

Protein Structure

Protein sequences of coronaviruses
https://webs.iiitd.edu.in/raghava/coronavir/prot.php

Nucleotide Sequence

Nucleotide sequences of coronaviruses
https://webs.iiitd.edu.in/raghava/coronavir/nucleotide.php

Drug Design

Potential Drug Targets

Potential drug targets which can be used for designing therapeutics against the recently emerged new strain of coronavirus i.e. Wuhan Coronavirus.
https://webs.iiitd.edu.in/raghava/coronavir/dt.php
https://webs.iiitd.edu.in/raghava/coronavir/dm.php

Potential Drug Molecules

Potential inhibitors which can be used as drug against newly emerged Wuhan coronavirus. The data was extracted by extensive literature search, and databases such as DrugBank
https://webs.iiitd.edu.in/raghava/coronavir/dm.php

#3D Protein Structures
Predicted tertiary structure of the proteins present in the Wuhan coronavirus. The proteins were modeled using Phyre 2.0 server and were further validated using PROCHECK server. Details of the template used for modeling the structure of proteins, percent similarity with the template, Fold of the template, its family and superfamily is provided.
https://webs.iiitd.edu.in/raghava/coronavir/struct.php

Predicted Cell Penetrating Peptides

Predicted potential Cell Penetrating Peptides (CPPs) which can be used for delivering small molecules, drug molecules, different types of cargo molecules, etc. These CPPs are part of the Wuhan coronavirus proteins and have been predicted using widely used server CellPPD
https://webs.iiitd.edu.in/raghava/coronavir/dd.php

GenBank

SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) Sequences
SARS-CoV-2 sequences currently available in GenBank
https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/

Additional Data Sources: