ProDom protein domain database

ProDom generates and organizes protein domain families by analyzing protein sequences from SWISS-PROT and TrEMBL (components of the UniProt Knowledgebase) to identify and classify recurring structural motifs.

Key Features:

• Automatic Generation: Employs an automated methodology to identify protein domain families from sequence data.
• Integration with SWISS-PROT and TrEMBL: Uses sequence data from SWISS-PROT and TrEMBL to represent a broad set of known protein sequences.
• ProDom-CG Extension: Applies domain analysis techniques to completed genomes for genome-scale domain annotation.
• Inclusion of Pfam-A Entries: Integrates expert-curated Pfam-A families to enrich and validate domain family assignments.
• Stable Accession Numbers: Assigns stable accession numbers to domain families for consistent referencing.
• Consistency Indicators: Provides indicators for assessing the consistency and robustness of domain families.
• Domain Arrangements and Sub-Families: Reports domain arrangements and sub-family structure to support detailed structural analysis.
• Links to Pfam-A: Supplies direct links to Pfam-A entries for cross-referencing expert-validated domain information.

Scientific Applications:

• Functional Annotation: Supports prediction of protein function by identifying conserved domains within sequences.
• Comparative Genomics: Enables analysis of domain composition across genomes using ProDom-CG to study evolutionary conservation.
• Protein Engineering: Informs protein design and modification by detailing domain arrangements and their variations.

Methodology:

ProDom systematically analyzes protein sequences from SWISS-PROT and TrEMBL to detect recurring structural motifs, groups these motifs into families based on sequence similarity, and integrates Pfam-A entries for expert-validated family assignments.