ProtCID

ProtCID clusters similar protein-protein interfaces across multiple crystal forms using PFAM domain architectures to identify conserved interaction patterns and support evolutionary and structural analysis.

Key Features:

• Interface clustering: Groups similar protein-protein interfaces across multiple crystal forms into clusters.
• PFAM domain-based grouping: Groups protein chains according to PFAM domain architectures to enable homologous comparisons.
• Cross-crystal-form comparison: Compares interfaces observed in different crystal forms to identify recurring interaction patterns.
• Heterodimer analysis: Applies the clustering approach to heterodimers with differing domain architectures.
• Cluster repository: Stores clustered interfaces within a database for comparative structural analysis.

Scientific Applications:

• Protein evolution studies: Identifies conserved and divergent interaction patterns to inform evolutionary analyses of protein interactions.
• Structural biology research: Supports exploration of interaction mechanisms and the impact of structural variations on function.
• Biological assembly annotation: Enhances annotation and validation of biological assemblies in databases such as PDB and PISA.

Methodology:

Groups protein chains by PFAM domain architectures and compares interfaces across multiple crystal forms to form clusters; the same approach is applied to heterodimers with differing domain architectures.