Confidence Is Local
A protein model can look finished while a loop is effectively unresolved. One global score also says little about interfaces, domain placement, or atomic clashes.
structuregrade parses PDB coordinates and AlphaFold-style pLDDT values from B-factors, groups atoms into residues, reports confidence bands, and runs an inter-residue clash screen.
Turn Color Into A Gate
The report exposes residue count, chain count, mean confidence, low-confidence residues, clash count, and an explainable grade. It is available through one engine shared by the CLI, API, workbench, and regression tests.
The Demo
The eight-residue fixture receives grade C: mean pLDDT 71.88, two residues at or above 90, two below 50, and no inter-residue clashes.
This is a triage gate, not structural validation. PAE is still required for relative domain placement and interfaces, and experimental evidence remains decisive.
Research Basis
AlphaFold's own confidence guidance treats pLDDT as a per-residue local confidence measure and recommends PAE for relative placement of domains.
Read the AlphaFold confidence guidance.