How would you assess confidence in a predicted protein structure?

Why

Inspect pLDDT residue by residue and use PAE to assess relative domain or chain placement. High pLDDT suggests locally consistent geometry but says less about dynamic states, ligands, cofactors or mutation effects. Review template and sequence coverage, biological assembly, disordered regions and any known experimental structures.

If using the model to design a binding experiment, focus on confidence at the proposed interface rather than the mean confidence of the whole protein. Compare candidate binding sites with sequence conservation, known functional residues and, when available, experimental maps. For example, two high-confidence domains may have large inter-domain PAE, making an inter-domain pocket speculative.

Report the version of the model and limitations explicitly and prioritize structural predictions for testable experiments, not definitive causal claims.