PPISearch

PPISearch identifies homologous protein-protein interactions (PPIs) across multiple species using BLASTP and annotated PPI databases to discover PPI families and infer conserved domain-domain and function-function transferability via Pfam, InterPro, and Gene Ontology (GO) annotations.

Key Features:

• Homology Identification: Uses BLASTP to scan an annotated database of 290,137 PPIs across 576 species compiled from five public databases to identify homologous families for a given query protein pair.
• Transferability Inference: Infers transferability of interacting domains and functions by identifying conserved domain-domain pairs using Pfam and InterPro annotations and conserved function pairs using GO annotations.
• Quantified Accuracy: Reports transferability rates of 88% for conserved domain-domain pairs across 103,762 PPI queries and 69% for conserved function pairs across 106,997 PPI queries.

Scientific Applications:

• Functional Annotation: Infers functions of uncharacterized proteins based on homologous PPIs and conserved function pairs annotated by GO.
• Evolutionary Studies: Analyzes conservation of domain-domain and function-function pairs across species to investigate conserved interaction mechanisms.
• Drug Discovery: Identifies conserved interaction networks and potential targets by mapping homologous PPIs and conserved domain interactions.

Methodology:

Uses BLASTP to search an annotated PPI database; determines homologous protein pairs based on significant joint sequence similarity (E ≤ 10^(-40)); and infers conserved domain-domain and function-function pairs using Pfam, InterPro, and GO annotations.