COPS

COPS classifies protein structures by encoding pairwise structural similarities as metric relationships and organizing them into a hierarchical fold space for analysis of structural domains.

Key Features:

• Comprehensive structural collection: Provides access to the entire collection of known protein structures and their structural domains.
• Metric similarity encoding: Quantifies pairwise structural similarities as metric relationships.
• Hierarchical tree organization: Organizes metric relationships into a hierarchical tree that represents fold space.
• Fold Space Navigator representation: Represents the hierarchical fold-space organization analogous to a filesystem for navigating structural relationships.
• Automated domain segmentation and placement: Newly determined protein structures are automatically segmented into domains and their locations within the hierarchical tree are identified.
• PDB synchronization: The dataset is updated weekly to remain synchronized with the Protein Data Bank (PDB).
• Visualization of domain similarities: Supports visualization and inspection of protein domain similarities.

Scientific Applications:

• Structural biology: Comparative analysis of protein structural domains and fold relationships.
• Bioinformatics: Computational analysis of structural datasets and domain organization.
• Evolutionary studies: Investigation of evolutionary relationships using structural similarity metrics.
• Functional annotation: Support for functional inference through structural and domain context.
• Drug discovery: Structural comparison of targets and domains to inform drug-design hypotheses.
• Structure–function analysis: Examination of protein structure–function relationships via domain similarity inspection.

Methodology:

Pairwise structural similarities are quantified as metric relationships and organized into a hierarchical tree; newly determined structures are automatically segmented into domains and placed within that tree; the dataset is updated weekly to synchronize with the Protein Data Bank (PDB).