CAPS-DB

CAPS-DB catalogs and classifies helix-capping regions (Nt- (N-terminal) and Ct- (C-terminal) cappings) in protein structures to analyze structural motifs and amino-acid type preferences that stabilize α-helices where intrahelical hydrogen bonds are absent in terminal turns.

Key Features:

• Helix-capping coverage: Catalogs Nt- (N-terminal) and Ct- (C-terminal) cappings associated with α-helices, focusing on regions that compensate for missing intrahelical hydrogen bonds in the first and last turns.
• Structural pattern organization: Organizes caps based on structural patterns derived from experimentally determined protein structures.
• Hierarchical classification: Implements a hierarchical classification system that reflects geometric and conformational properties of capping regions.
• Clustering algorithm: Uses a clustering algorithm that considers both geometry and (Φ-ψ)-space conformations of capping regions.
• Sequence-structure analysis: Annotates amino-acid type preferences linked to corresponding structural motifs of caps.
• Relational storage: Stores organized structural data in a relational database schema.

Scientific Applications:

• Protein design and engineering: Provides motif and amino-acid preference data to inform design choices for helix stabilization.
• Structural biology: Enables analysis of helix-capping geometry and conformational variability in protein structures.
• Bioinformatics: Supports comparative analyses of sequence-structure relationships and motif classification across protein datasets.

Methodology:

Classification is derived from structural patterns in protein structures via a hierarchical classification built from a clustering algorithm that considers geometry and (Φ-ψ)-space conformations, with data organized in a relational database.