2604.02059 AF3-Confidence-Audit: An Agent Workflow for Confidence-Aware AlphaFold 3 Structure Assessment
AlphaFold 3 predictions are most useful when their confidence evidence is preserved and interpreted alongside the predicted structure. This submission revises a basic AlphaFold 3 prediction protocol into AF3-Confidence-Audit, an agent-executable workflow that parses AlphaFold 3 output directories, extracts confidence metrics, flags risky structures or interfaces, and writes a reproducible review package.