PDBeFold

PDBeFold compares protein structures by aligning secondary-structure elements and iteratively superposing backbone Cα atoms using the SSM (Structure-Alignment) algorithm to identify structural similarities.

Key Features:

• SSM (Structure-Alignment) algorithm: Implements the SSM algorithm for three-dimensional protein structure comparison.
• Secondary-structure element matching graphs: Constructs matching graphs based on secondary-structure elements to identify correspondences between proteins.
• Iterative backbone Cα alignment: Performs iterative alignment and superposition of protein backbone Cα atoms to refine structural alignments.
• Balanced scoring (r.m.s.d. and Nalign): Uses a novel score that balances r.m.s.d. with alignment length (Nalign) to evaluate structural similarity.
• Cross-server agreement: Demonstrates reasonable agreement across different servers despite variations in r.m.s.d. and Nalign values.

Scientific Applications:

• Homolog detection: Identifies homologous proteins through structural alignment.
• Protein function and evolution analysis: Provides insights into protein function and evolutionary relationships from structural similarity.
• Drug design: Supports drug design by comparing protein structures to identify relevant structural relationships.
• Enzyme engineering: Aids enzyme engineering by comparing enzyme structures to inform engineering strategies.
• Disease mechanism characterization: Contributes to understanding disease mechanisms at a molecular level by comparing disease-related protein structures.
• Cross-database structural comparison: Enables comparison of structures across databases to detect structural relationships.

Methodology:

Constructs matching graphs from secondary-structure elements, applies the SSM (Structure-Alignment) algorithm for three-dimensional comparison, iteratively aligns backbone Cα atoms, and scores alignments by balancing r.m.s.d. with alignment length (Nalign).