SWORD2

SWORD2 partitions protein structures into hierarchical Protein Units to delineate structural domains, subdomains, and supersecondary structures for functional and evolutionary analysis.

Key Features:

• Hierarchical partitioning: Partitions protein structures into nested Protein Units representing multiple structural scales.
• Domain and substructure detection: Identifies structural domains, subdomains, and supersecondary structures as discrete fragments.
• Protein Peeling integration: Incorporates protein peeling methodology to inform structural decomposition.
• Model quality assessment: Applies model quality assessment measures to evaluate the relevance of partitioned substructures.
• Multiple partitioning solutions: Generates alternative partitioning solutions and evaluates identified substructures using various measures.

Scientific Applications:

• Functional region identification: Pinpoints regions that may correspond to independent folding units, catalytic or binding activities, or evolutionary modules.
• Domain delineation for structural biology: Supports delineation of structural domains to aid studies of protein function, origin, and evolution.
• Dataset construction: Enables construction of comprehensive, multilevel datasets of protein structures for bioinformatics analyses.

Methodology:

Performs a hierarchical assembly process to partition structures into Protein Units, integrates protein peeling and model quality assessment approaches, and generates multiple partitioning solutions whose substructures are evaluated using various measures.