DOMMINO

DOMMINO provides a curated database of macromolecular interactions covering structured domains, interdomain linkers, N- and C-terminal regions, and peptides to support structural analysis of protein-protein interfaces.

Key Features:

• Comprehensive Interaction Database: Catalogs interactions among protein domains, interdomain linkers, N- and C-terminal sequences, and peptides derived from macromolecular complexes.
• Integration with SCOP and SUPERFAMILY: Complements SCOP domain annotations by incorporating domain predictions from SUPERFAMILY for comparative and evolutionary analyses.
• Regular Updates: Dataset is maintained with weekly updates to incorporate newly resolved structures of macromolecular complexes.
• Flexible Search Criteria: Supports queries by PDB ID, interaction type, SCOP family, organism name, interaction keyword, and a minimal threshold on contact pairs.
• Subunit Interaction Network Visualization: Generates network representations of interactions within macromolecular assemblies at the subunit level.
• Interface Structure Representation: Provides interface-level structural representations of binary complexes with residue-type highlighting and interface detail.

Scientific Applications:

• Structural characterization of protein-protein interactions: Enables analysis of interfaces involving domains, linkers, terminal regions, and peptides.
• Evolutionary and comparative analysis: Uses SCOP annotations and SUPERFAMILY predictions to investigate evolutionary relationships among proteins.
• Interface-level mechanistic studies: Facilitates examination of contact pairs and interface residues for mechanistic interpretation of macromolecular complexes.

Methodology:

Integration of SCOP domain annotations and SUPERFAMILY domain predictions; weekly updates of interaction data; indexing and search by PDB ID, interaction type, SCOP family, organism name, interaction keyword, and contact-pair thresholds; generation of subunit interaction networks and interface-level structural representations with residue highlighting for binary complexes.