Scop3d

Scop3d maps sequence conservation and entropy onto protein 3D structures to integrate sequence variation with structural data for evolutionary and immunogenicity analysis.

Key Features:

• Automatic Integration: Aligns sequence variants, computes per-position conservation, and maps these metrics onto protein 3D structures.
• Output Files: Produces two modified PDB files in which traditional B-values are replaced by percentage sequence conservation and information entropy for each position.
• Comprehensive Data Output: Exports text files reporting absolute and relative amino acid occurrences at each position and generates visual snapshots from six distinct spatial orientations.
• Visualization: Displays regions of high sequence conservation or variability on the structure to facilitate identification of functional domains and antigenic sites.

Scientific Applications:

• Vaccine Development: Identifies conserved and potentially immunogenic protein regions to inform selection of vaccine targets.
• Antigenic Hotspot Identification: Visualizes conservation on viral proteins, including human respiratory syncytial virus and mumps virus fusion proteins, to locate potential antigenic hotspots.

Methodology:

Performs multiple sequence alignment of variants, calculates position-specific percentage conservation and information entropy, maps these metrics into PDB B-value fields, and outputs per-position amino acid frequency tables and six structural snapshots.