Waggawagga

Waggawagga predicts and visualizes coiled-coil regions and detects stable single α-helix (SAH) domains in protein sequences for comparative structural analysis.

Key Features:

• Comparative visualization: Provides overview schemes of predicted coiled-coil regions and helical wheel and helical net views for detailed structural interpretation.
• SAH domain prediction: Implements a window-based scoring system to detect stable single α-helix (SAH) domains, which are enriched in charged amino acids and noted as rigid connectors or constant-force springs between structural domains.
• Export capabilities: Exports visualizations to bitmap and vector graphics formats.
• Waggawagga-CLI: Enables genome-wide analyses of SAH domains across eukaryotic protein sequence datasets.
• Customizable analysis: Allows adjustment of scoring parameters for amino acid interactions at i,i+3 and i,i+4 spacings.

Scientific Applications:

• SAH domain identification: Identifies SAH domains in protein sequences to support studies of structural elements in multi-domain proteins.
• Protein architecture studies: Enables investigation of SAH domains as structural building blocks and their prevalence in longer eukaryotic proteins.
• Functional enrichment analysis (yeast): Facilitates gene ontology analyses showing enrichment of yeast SAH-containing proteins in macromolecular complex subunit organization and RNA metabolic processes.
• Human protein function associations: Supports association of SAH domains in human proteins with RNA processing activities and cytoskeleton organization.

Methodology:

Computational methods explicitly include comparative coiled-coil prediction visualization, helical wheel and helical net renderings, a window-based scoring system for SAH detection, adjustable scoring parameters for i,i+3 and i,i+4 amino acid interactions, and genome-wide scanning of protein sequence datasets.