PRINTS protein motif fingerprint database

PRINTS protein motif fingerprint database catalogs protein fingerprints composed of conserved sequence motifs to characterize protein families and annotate protein structure–function relationships.

Key Features:

• Non-overlapping Motifs: Motifs in a fingerprint typically do not overlap along the sequence but may be contiguous in three-dimensional structure.
• Iterative Database Scanning: Motif diagnostic power is refined by iterative scanning against composite databases, including OWL, to maximize sequence information.
• Independent Motif Identification: The approach identifies independent motifs that can be linearly or spatially separated to characterize specific protein folds and functionalities.
• Comparative Advantage: Fingerprints comprising multiple motifs provide more effective characterization than single-component patterns or regular expressions.
• Comprehensive Coverage: PRINTS version 4.0 includes over 150 entries encoding more than 700 motifs covering globular proteins, membrane proteins, and modular polypeptides.

Scientific Applications:

• Protein family characterization: Identification of conserved motif fingerprints for defining and distinguishing protein families.
• Structure–function analysis: Mapping motifs that may be contiguous in 3D to investigate protein structure–function relationships.
• Evolutionary biology: Analysis of conserved motifs across diverse proteins to study evolutionary relationships.
• Bioinformatics method development: Use of motif fingerprints and iterative scanning strategies in developing new computational annotation methods.
• Resource complementarity: Provides complementary motif annotations to resources such as PROSITE for broader protein motif analysis.

Methodology:

Motifs are extracted from conserved regions within sequence alignments and their diagnostic power is refined through iterative scanning against composite databases such as OWL to identify independent, non-overlapping motifs.