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.
The Clash Screen Was Flagging Every Normal Bond
The clash check excluded atom pairs within the same residue, but never excluded the one bond that legitimately spans a residue boundary: the peptide bond connecting each residue's carbon to the next residue's nitrogen, which sits around 1.33 Å — comfortably inside the 1.5 Å threshold this tool treated as a clash. The demo fixture only ever uses a single C-alpha atom per residue, so it never exercised this bond and never exposed the bug. Feed it a real, full-atom AlphaFold structure and every adjacent residue pair in the backbone would get flagged as colliding.
Verified directly: a two-residue backbone built with completely standard bond geometry — nothing structurally wrong with it at all — was reported as having one clash and downgraded from what should be an A to a C. Fixed by excluding specifically the C(i)–N(i+1) peptide-bond pair between sequentially adjacent residues in the same chain, while every genuine non-bonded steric clash between any other atom pair is still caught exactly as before.
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.