Coronavirus Reverse Engineering

The idea of this repo is to compile as much information as possible about the the coronavirus family, in particular about SARS-CoV-2. This includes genome sequences, protein structures and other resources available online.

Initial exploratory analysis it's on the root notebook from where we branch to other aspects of the virus.

TABLE OF CONTENTS

1. Genome Exploratory Analysis
2. Protein Recognition and Classification with Machine Learning
3. Machine Learning for Genus Classification

Useful Resources and References

• Coronaviruses (general overview)

  • Coronaviruses: An Overview of Their Replication and Pathogenesis
  • Coronavirus Main Proteinase (3CLpro) Structure: Basis for Design of Anti-SARS Drugs
  • COVID-19 infection: Origin, transmission, and characteristics of human coronaviruses
  • The coronavirus replicase
  • Coronavirus: RNA proofreading machine regulates replication fidelity and diversity
  • Coronavirus Genomics
  • The role of programmed-1 ribosomal frameshifting in coronavirus propagation
  • The origin, transmission and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak – an update on the status
  • Complete genome characterisation of a novel coronavirus associated with severe human respiratory disease in Wuhan, China
  • Interesting analysis of the evolution and adapatation of the Hepatitis E virus: Genotype-specific acquisition, evolution and adaptation of characteristic mutations in hepatitis E virus
  • Complete Genomic Sequence of Human Coronavirus OC43: Molecular Clock Analysis Suggests a Relatively Recent Zoonotic Coronavirus Transmission Event
  • Identification and characterization of Coronaviridae genomes from Vietnamese bats and rats based on conserved protein domains

• Coronavirus main protease. Is there a way to predict the cleavage sites in the orf1ab protein?

  • In Silico Analysis of ORF1ab in Coronavirus
  • Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors
  • Coronavirus 3CLproproteinase cleavage sites: Possible relevance to SARS virus pathology
  • Not from the Corona family, but the technique is relevant: Cleavage site analysis in picornaviral polyproteins: Discovering cellular targets by neural networks
  • Also not Corona related, but the same techniques can be used : Prediction of HIV-1 protease cleavage site using a combination of sequence, structural, and physicochemical features

• Potential drugs?

  • Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2