CoV3D

CoV3D provides access to curated high-resolution coronavirus protein structures and associated structural analyses to support structure-based vaccine and therapeutic design.

Key Features:

• Comprehensive structural collection: Curated set of coronavirus protein structures including spike glycoprotein complexes with antibodies, receptors, and small molecules.
• Spike glycoprotein emphasis: Focused representation of spike protein structures and spike–antibody complexes with annotated sequence variability and known polymorphisms.
• N-glycosylation modeling: Modeling of N-glycosylation at known glycan sites on spike glycoproteins to assess glycan placement and coverage.
• Structure-based classification: Generation of a structure-based classification of spike conformations using unsupervised clustering techniques.
• Visualization-capable structural data: Structural coordinates provided with support for mapping sequence variation and molecular interactions onto three-dimensional models.

Scientific Applications:

• Vaccine immunogen design: Inform selection and engineering of spike immunogens by relating structural conformations, glycosylation, and sequence polymorphisms to antigenicity.
• Therapeutic and small-molecule development: Support structure-based drug and antibody design by providing atomic-detail complexes of viral proteins with antibodies, receptors, and ligands.
• Neutralization mechanism analysis: Enable analysis of molecular interactions underlying virus neutralization through inspection of spike–antibody and spike–receptor interfaces.
• Comparative coronavirus structural studies: Facilitate comparative analysis across coronaviruses by providing a centralized set of experimentally determined protein structures.

Methodology:

Unsupervised clustering of spike structures to classify conformations; modeling of N-glycosylation at annotated glycan sites; mapping of sequence variability and known polymorphisms onto structural coordinates.