CUPSAT

CUPSAT predicts changes in protein stability caused by single amino acid substitutions by calculating the change in free energy of unfolding (ΔΔG) using structural environment-specific atom potentials and torsion angle potentials.

Key Features:

• Input format: Accepts protein structure files in PDB format together with a specified residue location for mutation analysis.
• ΔΔG calculation: Calculates the change in free energy of unfolding (ΔΔG) between wild-type and mutant proteins.
• Potentials used: Employs structural environment-specific atom potentials and torsion angle potentials for stability prediction.
• Torsion-angle adaptation assessment: Evaluates how well mutated amino acids can adopt observed torsion angles at the mutation site.
• Site structural features: Reports solvent accessibility, secondary structure, and torsion angles for the mutation site.
• Comprehensive substitution scanning: Provides stability predictions for all 19 possible amino acid substitutions at a given position.
• Validation and performance: Validated with split-sample, jack-knife, and k-fold cross-validation on datasets of 1538 thermal denaturation and 1603 chemical denaturation mutations, with >80% prediction accuracy in most tests.

Scientific Applications:

• Protein design: Supports protein design by predicting stability effects of single amino acid substitutions.
• Stability analysis: Enables analysis and ranking of point mutations based on predicted ΔΔG.
• Interpretation of denaturation data: Aids interpretation of mutation effects in thermal and chemical denaturation experimental datasets.

Methodology:

Calculates ΔΔG using structural environment-specific atom potentials and torsion angle potentials, assesses mutated residue compatibility with observed torsion angles, and was validated using split-sample, jack-knife, and k-fold cross-validation on datasets of 1538 thermal and 1603 chemical denaturation mutations.