TOPS

TOPS provides detailed topological descriptions of protein structures by abstracting three-dimensional folds into sequences of secondary structure elements (SSEs) and their pairwise relationships to support structural analysis.

Key Features:

• Topological Descriptions: Represents folds as sequences of SSEs (alpha helices and beta strands) with three sets of pairwise relationships based on hydrogen bonds between parallel and antiparallel beta strands, spatial adjacencies, and chiralities in selected supersecondary motifs (e.g., beta-alpha-beta and parallel alpha helices).
• Helix Packing Relationships: Incorporates packing relationships between helices to refine topological descriptions of folds with limited beta-strand content.
• Sequence Annotation: Annotates topological descriptions with amino acid sequence information.
• Topological Pattern Searching and Structure Comparison: Enables fast topological pattern searches and comparisons between protein structures.

Scientific Applications:

• Visualization of Folding Topologies: Enables visualization of protein folding topologies using SSE-based abstractions.
• Pattern Searching: Facilitates identification of recurring topological motifs across proteins via topological pattern searches.
• Structure Comparison: Supports precise comparisons of protein topology for evolutionary and functional analyses.

Methodology:

Abstracts 3D protein structures into sequences of SSEs and three sets of pairwise relationships (hydrogen-bonded beta-strand pairings, spatial adjacencies, and chiralities), incorporates helix packing relationships, and annotates these topological representations with sequence information.