PTGL

PTGL represents protein secondary structure topologies as undirected labeled graphs to enable classification and analysis of relationships between protein structure and function.

Key Features:

• Unique Representation: Protein topologies are represented as undirected labeled graphs in four distinct ways.
• Visualization: Provides linear notations, 2D topology diagrams and 3D structural visualizations for each notation.
• Search Capabilities: Supports queries for specific topologies and sub-topologies and enables BLAST searches for homologous sequences.
• Database Integration: Cross-references entries with SCOP, CATH, and PDBsum.
• Pre-implemented Structural Patterns: Includes predefined topologies for motifs such as the TIM-barrel and Jelly Roll.
• Dataset Coverage: Contains topologies for 54,859 protein structures.

Scientific Applications:

• Structure–Function Analysis: Classification and comparative analysis of protein structure–function relationships using topology graphs.
• Motif Identification: Identification and analysis of common structural motifs such as TIM-barrel and Jelly Roll across datasets.
• Large-scale Comparative Studies: Enables large-scale investigations and fast searches through extensive topology datasets to explore protein architecture.
• Homology Detection: Supports detection of homologous sequences and related structures via BLAST-integrated searches.

Methodology:

Represents protein secondary structure topologies as undirected labeled graphs using four distinct graph notations to abstract structural data, enabling classification perspectives beyond SCOP, CATH, and TOPS.