Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning

Nucleic Acids Res. 2021 Jul 2;49(W1):W671-W678. doi: 10.1093/nar/gkab279.

Abstract

Vaccination is one of the most significant inventions in medicine. Reverse vaccinology (RV) is a state-of-the-art technique to predict vaccine candidates from pathogen's genome(s). To promote vaccine development, we updated Vaxign2, the first web-based vaccine design program using reverse vaccinology with machine learning. Vaxign2 is a comprehensive web server for rational vaccine design, consisting of predictive and computational workflow components. The predictive part includes the original Vaxign filtering-based method and a new machine learning-based method, Vaxign-ML. The benchmarking results using a validation dataset showed that Vaxign-ML had superior prediction performance compared to other RV tools. Besides the prediction component, Vaxign2 implemented various post-prediction analyses to significantly enhance users' capability to refine the prediction results based on different vaccine design rationales and considerably reduce user time to analyze the Vaxign/Vaxign-ML prediction results. Users provide proteome sequences as input data, select candidates based on Vaxign outputs and Vaxign-ML scores, and perform post-prediction analysis. Vaxign2 also includes precomputed results from approximately 1 million proteins in 398 proteomes of 36 pathogens. As a demonstration, Vaxign2 was used to effectively analyse SARS-CoV-2, the coronavirus causing COVID-19. The comprehensive framework of Vaxign2 can support better and more rational vaccine design. Vaxign2 is publicly accessible at http://www.violinet.org/vaxign2.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antigens, Viral / chemistry
  • Antigens, Viral / immunology
  • COVID-19 / virology
  • COVID-19 Vaccines / chemistry
  • COVID-19 Vaccines / immunology
  • Drug Design*
  • Epitopes / chemistry
  • Epitopes / immunology
  • Humans
  • Internet*
  • Machine Learning*
  • Proteome
  • SARS-CoV-2 / chemistry
  • SARS-CoV-2 / immunology
  • SARS-CoV-2 / metabolism
  • Software*
  • Spike Glycoprotein, Coronavirus / chemistry
  • Spike Glycoprotein, Coronavirus / immunology
  • Vaccines* / chemistry
  • Vaccines* / immunology
  • Vaccinology / methods*
  • Workflow

Substances

  • Antigens, Viral
  • COVID-19 Vaccines
  • Epitopes
  • Proteome
  • Spike Glycoprotein, Coronavirus
  • Vaccines
  • spike protein, SARS-CoV-2