iSOCKET

iSOCKET analyzes side-chain packing to identify α-helical coiled coils and classify their architectures using graph-theory-based methods.

Key Features:

• Side-chain packing analysis: Identifies and analyzes side-chain packing interactions within protein structures.
• Automatic coiled-coil identification: Automatically detects α-helical coiled coils in experimentally characterized protein structures.
• Graph-theory Atlas classification: Applies graph-theory methodologies to implement an Atlas classification scheme for categorizing coiled-coil substructures.
• Atlas of Coiled Coils and enumeration: Generates an Atlas of Coiled Coils that includes known structures and a partial enumeration of theoretically possible but unobserved coiled-coil architectures.

Scientific Applications:

• Protein structure and folding analysis: Provides insights into side-chain packing that inform understanding of protein structure, folding, and function for α-helical coiled coils.
• Classification of coiled-coil subclasses: Identifies and classifies emerging subclasses such as α-helical barrels within coiled-coil families.
• De novo protein design targets: Maps observed and theoretical coiled-coil architectures, including theoretical "dark matter" architectures, to define targets for de novo protein design and protein engineering.
• Systematic organization of substructures: Systematically categorizes coiled-coil substructures to support analysis of protein architecture complexity.

Methodology:

Detects side-chain packing interactions, automatically identifies α-helical coiled coils, applies graph-theory-based methods to implement an Atlas classification scheme, and generates atlases including a partial enumeration of theoretical coiled-coil architectures.