PPI3D

PPI3D predicts three-dimensional structures of protein complexes using template-based modeling to map protein–protein interactions onto homologous structural templates.

Key Features:

• Template-Based Modeling: Predicts individual protein structures and multimeric complexes by using known homologous structures as templates.
• Homology Search Capabilities: Identifies suitable homologous protein complexes that can serve as structural templates for modeling.
• Interaction Analysis and Modeling: Analyzes interaction interfaces within identified complexes and models protein–protein interactions in 3D.
• Validation in Community Assessments: Has been applied and evaluated in CASP and CAPRI assessments for homology modeling of multimeric proteins.

Scientific Applications:

• Drug Discovery: Identifies interaction interfaces and potential binding sites to inform structure-guided drug design.
• Functional Genomics: Provides structural context for protein complexes to aid elucidation of gene function and regulation mechanisms.
• Structural Biology Research: Complements experimental structural data with computationally predicted models of protein complexes.

Methodology:

Identifies homologous protein complexes as templates and applies template-based modeling to predict individual protein structures and multimeric complexes, modeling interaction interfaces to generate 3D representations.