Simple modular architecture research tool (SMART)

Simple modular architecture research tool (SMART) identifies and annotates protein domains and analyzes protein domain architectures to support comparative, functional, and evolutionary studies.

Key Features:

• Manually Curated Domain Models: Contains over 1,200 manually curated domain models, including approximately 200 models added since the previous update.
• Data Integration and Synchronization: Synchronizes underlying protein databases with UniProt, Ensembl, and STRING, supporting annotation of over 100 million domains and other protein features.
• Genomic Annotation: Genomic mode annotates proteins from completely sequenced genomes across 2,031 species.
• Pathway and Interaction Network Integration: Integrates metabolic pathway data with links to pathway resources and provides an interaction network view covering over 2 million proteins.
• Advanced Search and Export: Provides a full-text search covering SMART and Pfam domain annotations and protein descriptions and supports export of domain architecture analysis results for visualization with iTOL.
• metaSMART: Facilitates exploration and analysis of domain architectures in metagenomics datasets.
• Novel Discoveries and Predictions: Enables prediction of novel domain homologues, previously unknown domain families, putative functions of domain families, cellular roles for proteins, signaling domains in disease genes, domains in unexpected phylogenetic contexts, and likely protein misclassifications.

Scientific Applications:

• Domain identification and annotation: Identifying and annotating protein domains within genomic and protein sequences.
• Comparative evolutionary analysis: Comparing domain architectures across species to infer evolutionary relationships.
• Signaling and interaction analysis: Investigating signaling pathways and protein interactions by analyzing multidomain proteins.
• Comparative genomics of domain combinations: Conducting comparative studies of domain combinations across organisms.
• Metagenomics domain architecture analysis: Analyzing metagenomics datasets to characterize domain architectures in environmental samples.

Methodology:

Manual curation of domain models; synchronization of underlying protein databases with UniProt, Ensembl, and STRING; Genomic mode annotation of proteins from completely sequenced genomes (2,031 species); integration of metabolic pathway data and interaction networks covering over 2 million proteins; full-text search across SMART and Pfam annotations; metaSMART analysis for metagenomics domain architectures; export of domain architecture results for visualization with iTOL.