Jupytope

Jupytope extracts structural properties of viral epitopes to support immunological analyses such as vaccine development, disease diagnosis, and drug design.

Key Features:

• Integration with Biopython, NACCESS, and DSSP: Leverages Biopython modules and external programs NACCESS and DSSP to compute solvent accessibility and assign secondary structure.
• Comprehensive structural property extraction: Computes dihedral angles, solvent accessibility, residue depth, and secondary structure for specified epitope residues.
• Spatial alignment to reference structures: Aligns epitope sites with corresponding reference structures prior to property extraction to preserve spatial context.
• Data output flexibility: Exports extracted structural properties in multiple data formats for downstream analysis.

Scientific Applications:

• Vaccine Development: Provides structural characterisation of epitopes to inform identification of potential vaccine targets.
• Disease Diagnosis and Drug Design: Supports distinguishing viral strains and informing targeted therapeutic design using epitope structural signatures.
• Subtype and clade differentiation (Influenza and SARS-CoV-2): Enables comparison of epitope properties to differentiate viral subtypes and clades, as demonstrated with Influenza and SARS-CoV-2 examples.

Methodology:

Accepts a viral antigen structure, a list of epitope sites, and a reference structure; performs spatial alignment of epitopes to the reference; uses Biopython together with NACCESS and DSSP to extract dihedral angles, solvent accessibility, residue depth, and secondary structure; and outputs results in multiple data formats.