SSEP

SSEP provides detailed information about secondary structural elements of proteins from non-redundant Protein Data Bank (PDB)-derived datasets, enabling analysis of alpha-helices, beta-strands, 3(10)-helices, beta- and nu-turns, and hairpin loops.

Key Features:

• Non-redundant datasets: Provides two levels of non-redundancy derived from the PDB at 25% and 90% sequence identity.
• Secondary structure annotation: Contains annotations for alpha-helices, beta-strands, 3(10)-helices, beta- and nu-turns, and hairpin loops.
• Dataset size: Includes 2,485 protein chains in the 25% non-redundant set and 8,595 chains in the 90% non-redundant set.
• 3D visualization integration: Interfaces with RASMOL to enable three-dimensional visualization of queried secondary structural fragments.
• Comparative scope: Supports comparative analyses across diverse protein structures using curated non-redundant sets.

Scientific Applications:

• Structural biology: Facilitate analysis of protein secondary structure contributions to folding, stability, and function.
• Bioinformatics research: Enable large-scale analysis of secondary structure patterns across non-redundant PDB-derived datasets.
• Computational modeling: Provide secondary structure annotations that can inform modeling, validation, and interpretation of protein structures.
• Comparative structural analysis: Support comparative studies of secondary structural motifs across proteins at different redundancy levels.

Methodology:

Non-redundant datasets at 25% and 90% sequence identity are derived from the PDB and annotated for alpha-helices, beta-strands, 3(10)-helices, beta- and nu-turns, and hairpin loops, with integration for 3D visualization via RASMOL.