VanishPoint
Most AlphaFold viewers have a confidence lens: slide a threshold and the model fades away everywhere it is unsure, leaving only the parts it is confident about. It is tempting to read whatever fades first as “wrong” or “not important”. VanishPoint turns that lens into a game — predict where each region vanishes, then watch the lens sweep — and shows that a region can fade early and still be the working heart of the protein. Everything runs locally; nothing about you is collected.
This is the tool. For the trap regions, your reading is checked against the region’s live UniProt functional annotations, fetched in your browser. Every region is listed in full below (works without JavaScript). A native version, when it ships, adds offline use; it never gates the web.
Loading the game… If it does not start, the full region guide below still works.
How to play. Press Start. A region is highlighted in 3D. Predict how confident the model is there — 1 Very high, 2 Confident, 3 Low, 4 Very low. The lens sweeps up and the region fades at its true confidence, scoring your prediction. If it faded early, you are asked whether that means it does not matter (T/F) — and the live UniProt annotation settles it. Press Enter or Next to continue.
What the lens does: pLDDT confidence
AlphaFold scores every residue from 0 to 100 for how sure it is of the local shape — a score called pLDDT. The confidence lens simply hides everything below a threshold you choose. EMBL-EBI groups the score into four bands:
- Very high (pLDDT ≥ 90) — a backbone you can usually trust — stays crisp under the lens
- Confident (70–90) — a good guess at the fold
- Low (50–70) — treat the exact shape with caution
- Very low (< 50) — no single fixed shape on its own — fades first under the lens
The one idea to take away. When the lens hides a region, it means AlphaFold is not sure of the region’s exact shape on its own — most often because it is intrinsically disordered, or a flexible linker, or a part that only folds when it binds a partner (and, just occasionally, a genuinely hard prediction). None of those means the region is a mistake or unimportant — “flexible and functional”, not “wrong and useless”, is the expert’s starting point. Some of the most important regions in biology — like most of BRCA1, or the front end of c-Myc — fade first.
The regions
| Protein | Region | Residues | Confidence | What it does |
|---|---|---|---|---|
| BRCA1 P38398 | N-terminal RING domain | 24–64 | Very high | A zinc-binding fold that pairs with BARD1 to form the E3 ubiquitin-ligase — well determined, stays crisp. |
| BRCA1 P38398 | Central intrinsically-disordered region | 500–1000 | Very low · fades early, still functional | Most of BRCA1 is disordered — yet this middle is a working scaffold carrying binding sites and DNA-damage phosphorylation marks. Fades early, still essential. |
| BRCA1 P38398 | Tandem C-terminal BRCT domains | 1646–1859 | Very high | A phospho-peptide reader that docks onto partners once they are phosphorylated — well folded, stays crisp. |
| c-Myc P01106 | N-terminal transactivation region (MYC boxes I–II) | 1–143 | Very low · fades early, still functional | Disordered, and the business end — recruits co-activators through the conserved MYC boxes. Faded, but where the control happens. |
| c-Myc P01106 | C-terminal bHLH-leucine-zipper | 355–439 | Confident | The DNA-binding / dimerisation module — its helices are locally well-defined, so it stays fairly crisp, but it only grips DNA as a MYC–MAX pair. A crisp region can still need a partner to work. |
| Lysozyme C P61626 | Folded catalytic body | 19–148 | Very high | A compact, disulphide-stapled enzyme that cleaves bacterial cell-wall sugars — rigid, stays crisp all the way down. |
| Lysozyme C P61626 | N-terminal signal peptide | 1–18 | Low | Gets the enzyme exported, then is cleaved off — no fixed fold in the mature protein, so it is correctly faded. |
Methods & about
The 3D models are fetched live from the AlphaFold Database and coloured by pLDDT; for the trap regions the “still functional” reading is checked against the region’s live UniProt functional annotations. The confidence bands are a coarse per-region sketch of each model’s AlphaFold confidence (the teaching point is where a region sits on the confidence scale, not an exact number). The misconception it targets — that a faded, low-confidence region is a failure or does not matter — is a documented novice reading of the AlphaFold confidence colouring. Every region is written by hand, not generated, and science-checked. Nothing is stored; no accounts; no servers of ours (your browser talks straight to AFDB and UniProt).
Want to drive the lens on any structure yourself? Open the free AlphaFold viewer. Everything we make is free and non-profit; learn more on the home page.