pyDockEneRes

pyDockEneRes performs per-residue energy decomposition of protein–protein docking poses to quantify electrostatic, desolvation, and van der Waals energetic contributions and to estimate mutation-induced changes in binding affinity.

Key Features:

• Energy-based scoring function: Uses a scoring function derived from pyDock that integrates electrostatics, desolvation, and van der Waals energy terms to evaluate docking poses.
• Per-residue energy decomposition: Partitions docking energies at the residue level to identify energetically significant residues within interfaces.
• Side-chain contribution analysis: Computes the contribution of side-chain atoms to the overall docking energy.
• Mutation impact estimation: Estimates changes in binding affinity caused by mutations, including alanine substitutions.

Scientific Applications:

• Structural characterization: Provides residue-level energy profiles to support interpretation of protein–protein complex structures.
• Hot-spot identification: Identifies energetically relevant interface residues (hot-spots) that contribute disproportionately to binding energy.
• Binding affinity prediction: Predicts effects of mutations on binding affinity to inform experimental design and interpretation.

Methodology:

Calculates electrostatic, desolvation, and van der Waals energies using a pyDock-derived scoring function to evaluate docking poses; performs per-residue energy decomposition and computes side-chain atom contributions; estimates mutation-induced binding affinity changes such as alanine substitutions.