DomainCuts
Big proteins are built from smaller domains — compact folded units strung along the chain. AlphaFold’s 2026 companions (TED / CATH) carve the chain into these domains automatically. This game asks you to do it: first carve a chain into its domains, then judge how much to trust where those domains sit relative to each other. The twist: a model can be crisp (high confidence) in every domain and still be unsure of the arrangement — only the PAE shows that. Everything runs locally; nothing about you is collected.
This is the tool. The carve is scored against known domain boundaries; the trust answer is computed live from the model’s AlphaFold PAE matrix, fetched in your browser. Every protein and its domains are listed below (works without JavaScript).
Loading the game… If it does not start, the full domain guide below still works.
How to play. Press Start. Move the cursor (slider or ←/→) and press Drop cut (Enter) to place the domain boundaries, then Score the carve. Next, judge the domains’ relative placement — pick the pair the model is least sure about (or Confident/Uncertain for a two-domain protein) with the number keys — and the live PAE settles it. Press Enter or Next to continue.
Two different questions: pLDDT vs PAE
pLDDT asks “how sure is the model of the local shape here?” — it is high inside a well-folded domain. PAE (predicted aligned error) asks a different question: “if I line up on residue i, how sure am I of where residue j is?” Between two domains joined by a flexible hinge, PAE is large even when both domains are crisp. That gap — confident domains, uncertain arrangement — is the whole point of this game (misconception M04).
The proteins and their domains
| Protein | Length | Folded domains | Note |
|---|---|---|---|
| c-Src kinase P12931 Three folded domains that clamp together to switch the kinase off — a famous regulated arrangement. | 536 aa | SH3 (84–145) · SH2 (151–248) · Kinase (270–523) | Residues 1–83 are a disordered SH4 + unique tail, not a folded domain. |
| Abl1 tyrosine kinase P00519 The CML drug target (imatinib). Same SH3–SH2–kinase cassette as Src, then a very long disordered tail. | 1130 aa | SH3 (65–120) · SH2 (127–217) · Kinase (242–493) | Residues 494–1130 are a long, largely disordered C-terminal region. |
| Calmodulin P0DP23 Two calcium-sensing lobes on a floppy linker. Each lobe is crisp, yet the model is unsure how they sit relative to each other. | 149 aa | N-lobe (1–76) · C-lobe (81–148) | The two lobes are joined by a flexible central helix (~77–80) — the textbook flexible linker. |
Methods & about
Models and their PAE matrices are fetched live from the AlphaFold Database; the trust score is the mean inter-domain PAE computed in your browser (the same quantity AlphaFold’s own PAE plot shows). The domain ranges are a coarse but honest reading of the TED/CATH domain decomposition — the teaching point is where the boundaries fall and how the domains are arranged, not exact residue-perfect edges. Fibronectin (FN1), suggested in our concept census, is a beads-on-a-string of ~29 repeated modules — not a clean discrete carve — so calmodulin (two lobes on a flexible linker) stands in as the gold example of confident-domains-but-uncertain- arrangement. Every domain is written by hand, not generated, and science-checked. No accounts, no storage, no servers of ours.
Want to see PAE for any structure yourself? Open the free AlphaFold viewer. Everything we make is free and non-profit; learn more on the home page.