Protein Binding Evaluation (PROBE)

Protein Binding Evaluation (PROBE) refines docking poses and applies regression-based scoring that integrates geometric compatibility and normalized interaction energy to prioritize native-like protein–protein interface models.

Key Features:

• Refinement and Scoring: Refines structural configurations of pruned docking poses to improve geometric compatibility with known protein–protein interfaces.
• Ranking Using Regression Models: Ranks refined poses using a regression model that integrates geometric compatibility and normalized interaction energy.
• Integration in Docking Workflow: Operates downstream of the PRUNE service, which selects a subset of docking poses based on an interface area-based edge-scoring function.
• Single-Parameter Preselection: Leverages PRUNE's single-parameter elimination to reduce the pose set and increase the likelihood of native-like models among top-ranked poses.

Scientific Applications:

• Structural biology and complex prediction: Improves prediction of the quaternary structure of protein complexes by refining and prioritizing docking poses.
• Mechanistic and disease-related interaction studies: Supports investigation of molecular mechanisms and disease-related protein–protein interactions by prioritizing native-like interface models.

Methodology:

Structural refinement of pruned docking poses; scoring with a regression model assessing geometric compatibility and normalized interaction energy; ranking of refined poses; initial pose selection by PRUNE using an interface area-based edge-scoring function and single-parameter elimination.