DHcL

DHcL analyzes protein domain structures by delineating an energy hierarchy and detecting closed loops and van der Waals locks to characterize domain organization.

Key Features:

• Hierarchical Domain Analysis: Identifies protein domains across multiple hierarchical levels based on energy considerations.
• Closed Loop and van der Waals Lock Detection: Detects closed loops and van der Waals locks within protein structures as stabilizing structural elements.
• Database of X-ray PDB-derived Domains: Maintains a database of domain decompositions, closed loops, and van der Waals locks derived from X-ray structures in the Protein Data Bank (PDB).

Scientific Applications:

• Domain decomposition analysis: Provides alternative domain decompositions for detailed study of protein architecture.
• Function and stability inference: Supports interpretation of protein function and structural stability via identified closed loops and van der Waals locks.
• Comparative structural analysis: Enables analysis of PDB X-ray structures for comparative studies of domain organization across proteins.

Methodology:

Uses an energy-hierarchy-based approach to delineate protein domains with explicit identification of closed loops and van der Waals locks.