DOMAINATION_Domain_Prediction

DOMAINATION_Domain_Prediction identifies structural domains in protein sequences and improves detection of distant homologs by segmenting multidomain proteins and performing iterative PSI-BLAST searches.

Key Features:

• Domain inference from local gapped alignments: Infers domains and their boundaries from local gapped alignments generated by PSI-BLAST.
• Recognition of domain insertions and permutations: Detects domain insertions and permutations to identify domains that vary in sequence or order.
• Iterative domain-level querying: Submits segmented domains as individual queries in successive iterative PSI-BLAST searches to refine distant homology detection.
• Performance on multidomain datasets: Evaluated on a dataset of 452 multidomain proteins, achieving 50% accuracy in predicting structural domain boundaries and a 14% improvement over PSI-BLAST in detecting distant homologs.

Scientific Applications:

• Protein structural domain annotation: Improves delineation of structural domains in multidomain proteins for structure–function studies.
• Evolutionary analysis: Enhances detection of distant homologs for evolutionary and comparative genomics investigations.
• Functional annotation and molecular genetics: Supports functional annotation by revealing modular protein architecture and distant homologous relationships.

Methodology:

Uses PSI-BLAST local gapped alignments to infer domain boundaries, recognizes domain insertions and permutations, and iteratively queries segmented domains as separate PSI-BLAST searches.