SARS-Arena

SARS-Arena is a computational pipeline designed to aid in developing novel vaccines against SARS-CoV-2 and related viruses. The tool identifies conserved regions in the nucleocapsid (N) protein, which is less susceptible to selection pressure than the spike protein targeted by most current vaccines. By analyzing the N protein, SARS-Arena aims to discover potential T-cell targets to elicit a robust immune response.

The pipeline combines sequence-based methods and structure-based analyses to perform the following tasks:

1. Multiple sequence alignment (MSA) of SARS-CoV-related N protein sequences to identify conserved regions.

2. Recovery of candidate peptides of varying lengths from the conserved protein regions.

3. Modeling the 3D structure of the conserved peptides in different Human Leukocyte Antigen (HLA) molecules.

Topic

Small molecules;Immunoproteins and antigens;Pathology;Immunoinformatics;Workflows

Detail

  • Operation: Protein-ligand docking;Peptide immunogenicity prediction;Epitope mapping

  • Software interface: Script,Command-line tool

  • Language: Python

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: National Science Foundation, Rice University, CPRIT, University of Houston, National Library of Medicine, NIH.

  • Input: -

  • Output: -

  • Contact: -

  • Collection: -

  • Maturity: -

Publications

  • SARS-Arena: Sequence and Structure-Guided Selection of Conserved Peptides from SARS-related Coronaviruses for Novel Vaccine Development.
  • Rigo MM, et al. SARS-Arena: Sequence and Structure-Guided Selection of Conserved Peptides from SARS-related Coronaviruses for Novel Vaccine Development. SARS-Arena: Sequence and Structure-Guided Selection of Conserved Peptides from SARS-related Coronaviruses for Novel Vaccine Development. 2022; 13:931155. doi: 10.3389/fimmu.2022.931155
  • https://doi.org/10.3389/FIMMU.2022.931155
  • PMID: 35903104
  • PMC: PMC9315150

Download and documentation

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