PCFamily

PCFamily identifies homologous protein complex families (PCFs) and infers binding models and functional modules for query proteins using template-based structural comparisons.

Key Features:

• Template-Based Identification: PCFamily identifies homologous protein complex families (PCFs) by running BLASTP against a structural template database of 11,263 protein complexes.
• Comprehensive Genomic Database Search: It searches the Integr8 genomic database containing sequences from over 6 million proteins across 2274 species to extend homologous complex detection.
• Inference of Binding Models and Functional Modules: By analyzing homologous complexes across multiple species, PCFamily infers binding models that include hydrogen bonds and conserved amino acids at interface sites and identifies functional modules and conserved interacting domains.
• Gene Ontology Annotations: PCFamily assigns Gene Ontology annotations to inferred protein complex families to characterize their biological roles.

Scientific Applications:

• Binding Model Visualization: Enables visualization and interpretation of binding models to examine molecular interactions including interface hydrogen bonds and conserved residues.
• Protein Annotation: Supports annotation of query proteins with functional insights derived from homologous complexes and conserved domains.
• Functional Module Determination: Reveals conserved functional modules and interacting domains across species to support comparative and evolutionary analyses.

Methodology:

PCFamily first identifies homologous structural complexes by running BLASTP against a structural template database of 11,263 protein complexes, then searches for these homologous complexes in the Integr8 genomic database (over 6 million proteins from 2274 species) and analyzes the homologous complexes across species to infer binding models (including hydrogen bonds and conserved interface amino acids), conserved interacting domains, functional modules, and Gene Ontology annotations.