SpikeScape

SpikeScape analyzes structural diversity of the SARS-CoV-2 spike glycoprotein by standardizing PDB chain and sequence numbering and computing distance distributions between specified atom pairs across spike structures, including wild-type, variant, 2P-substituted, antibody-bound, and RBD open/closed conformations while excluding fragment-only RBD entries.

Key Features:

• Chain Standardization: Standardizes chain and sequence numbering across PDB files to resolve inconsistencies that impede direct structural comparison.
• Distance Distribution Calculation: Computes distributions of distances between any two specified atoms across available SARS-CoV-2 spike structures in the PDB.
• Variant and State Handling: Processes structures representing wild-type spikes, different variants, 2P substitutions, antibody-bound states, and RBD closed/open conformations.
• Filtering Options: Applies filters based on criteria such as protein variants or bound molecules to refine analysis sets.
• Visualization of Distributions: Generates histograms and cumulative frequency plots for the calculated distance distributions.

Scientific Applications:

• Comparative structural analysis: Quantifies structural variation across SARS-CoV-2 spike structures to support comparative studies.
• Variant impact assessment: Evaluates how different variants and 2P substitutions alter spike geometry.
• Interaction analysis: Assesses structural impacts of antibody binding and RBD open versus closed conformations.
• Vaccine and therapeutic relevance: Provides quantitative measures of spike structural variability to inform vaccine design and therapeutic development.

Methodology:

Standardizes chain and sequence numbering across PDB entries, computes distributions of distances between specified atom pairs across SARS-CoV-2 spike structures (excluding fragment-only RBD entries), applies user-specified filters for variants or bound molecules, and generates histograms and cumulative frequency plots of the distance distributions.