VIPERdb

VIPERdb provides structured access to icosahedral virus capsid structural data and analytical representations to enable comparative structural bioinformatics of capsid proteins.

Key Features:

• Relational database: Relational database implementation with a schema specifically designed for macromolecular structures.
• Structural data integration: Integration of high-resolution crystal structures and cryo-electron microscopy (EM) structures.
• Phi-Psi (Φ-Ψ) diagrams: Azimuthal polar orthographic projections representing capsid protein residues within the icosahedral asymmetric unit (IAU).
• Residue classification: Mapping and categorization of residues into surface, interface, and core types using Phi-Psi diagrams.
• Conserved residues and hotspots: Identification and mapping of family-wide conserved residues and interface hotspots for comparative analyses.
• API: Application Programming Interface (API) enabling programmatic access and integration with other bioinformatics tools and databases.
• Visualization and alignment: Integration with Jmol and STRAP for molecular visualization and sequence-structure alignments.
• Curation: Rigorous curation practices to maintain data uniformity across the macromolecular structure dataset.

Scientific Applications:

• Comparative structural analysis: Comparative structural analyses of capsid proteins across virus families using conserved-residue and hotspot mapping.
• Functional site mapping: Mapping surface, interface, and core residues to infer functional and assembly-related sites.
• Sequence-structure correlation: Performing sequence-structure alignments to correlate sequence conservation with structural localization.
• Structural bioinformatics and modeling: Providing curated structural datasets for structural bioinformatics, modeling, and interface analysis.
• Automated integration: Enabling integration with external bioinformatics tools and databases via the API for automated analyses.

Methodology:

Representation of capsid residues via azimuthal polar orthographic projections (Phi-Psi (Φ-Ψ) diagrams) for the icosahedral asymmetric unit (IAU); mapping residues into surface, interface, and core types; identification of family-wide conserved residues and interface hotspots; relational database implementation with a macromolecular structure schema; integration of crystal and cryo-EM structures; programmatic access via an API; and visualization and sequence-structure alignments using Jmol and STRAP.