PRORATE

PRORATE predicts protein folding rates for both two-state and multi-state protein folding kinetics by integrating structural topology and complex network properties derived from protein three-dimensional structures.

Key Features:

• Folding-rate prediction: Predicts protein folding rates for both two-state and multi-state folding kinetics.
• Structural topology integration: Uses structural topology metrics derived from protein three-dimensional structures.
• Complex network properties: Incorporates complex network properties of residue interactions into predictions.
• Protein Contact Network (PCN): Models local interactions within the protein structure via a residue contact network.
• Long-range Interaction Network (LIN): Captures long-distance residue interactions to represent broader structural connectivity.
• Network-level insight: Provides insights into the network organization of interacting residues that underpin folding processes across kinetic states.
• Integrative performance: Employs an integrative strategy reported to demonstrate superior performance compared to existing prediction methods.

Scientific Applications:

• Complementary prediction: Serves as a complementary method to existing folding-rate prediction algorithms.
• Foldomics characterization: Enhances the characterization of foldomics protein data.
• Protein dynamics and stability studies: Applies to research on protein dynamics and stability across different kinetic states.

Methodology:

PRORATE utilizes two types of protein residue contact networks: Protein Contact Network (PCN), based on local interactions within the protein three-dimensional structure, and Long-range Interaction Network (LIN), which captures long-distance residue interactions to represent structural connectivity.