ARCTIC-3D

ARCTIC-3D retrieves and clusters protein interface information from 3D structural data to characterize and classify biological interfaces and generate restraints for integrative modelling.

Key Features:

• Data Mining from PDBe: Retrieves existing interface data from the PDBe graph database.
• 3D Structural Clustering: Groups similar interfaces based on three-dimensional structural information.
• Interface Complexity Analysis: Quantifies the number of different interfaces per protein, revealing that 20% of eukaryotic proteins have more than 3 different interfaces compared to 10% for prokaryotes.
• Recognition Entropy Calculation: Computes the number of possible interfaces of components in a protein-protein complex to estimate modelling difficulty in classical docking approaches.
• Restraint Generation: Generates various combinations of interface-specific restraints for integrative modelling of biomolecular assemblies.

Scientific Applications:

• Protein Interface Characterization: Classifies and characterizes existing biological interfaces from the protein structural interactome in the Protein Data Bank.
• Functional Annotation of Interfaces: Associates different biological functions to different interfaces of the same protein.
• Protein-Protein Docking Assessment: Uses recognition entropy to predict and correlate with modelling difficulty in classical docking approaches.
• Integrative Structural Modelling: Provides interface cluster-derived restraints for modelling biomolecular assemblies.
• Comparative Interface Complexity: Compares interaction complexity across organism types, such as eukaryotes versus prokaryotes.

Methodology:

ARCTIC-3D retrieves interface data from the PDBe graph database and clusters similar interfaces based on 3D structural information; the resulting interface clusters are used to generate combinations of interface-specific restraints.