Fold Commons

A printable classroom hand-out. Use your browser's Print (⌘/Ctrl-P) — each band prints on its own page, and the site chrome drops away. Scan any rung to open it.

The protein-structure route

One page, one path — from “a protein is a shape” to “why we trust a prediction.” Scan any rung to open it. Nothing here needs a login, and nothing about you is collected.

Languages: English now; the six other Spark & Anvil learner languages follow (the scanned link carries the language).

Ages 9-14

Start with a cell and its parts, and climb to how a protein's shape does its job and how a prediction can be sure in some places and unsure in others.

  1. 1 BioForge Spark & Anvil

    Cells have parts, and proteins do most of the work.

    https://sparkanvil.org

  2. 2 Junior explorer Fold Commons

    A protein is a 3D shape, not a line of letters.

    https://foldcommons.org/junior/explore

  3. 3 ProteinQuest Fold Commons

    The shape is built from twenty amino acids that differ in character - some shun water, some love it.

    https://foldcommons.org/tools/proteinquest

  4. 4 TraitForge Spark & Anvil

    DNA -> mRNA -> codon -> amino acid; one changed letter can change one amino acid.

    https://sparkanvil.org

  5. 5 NotMarbles Fold Commons

    The shape does the job, and shapes move and change when they bind - they are not rigid and not a line.

    https://foldcommons.org/tools/notmarbles

  6. 6 VanishPoint Fold Commons

    A predicted model is sure of its shape in some places and unsure in others - four honest colours.

    https://foldcommons.org/tools/vanishpoint

  7. 7 DisorderDuty Fold Commons

    "Fuzzy" can mean disordered-and-working, not wrong.

    https://foldcommons.org/tools/disorderduty

  8. 8 MicrobeLab Spark & Anvil

    Proteins recognise each other - antibodies, receptors - the bridge to interfaces.

    https://sparkanvil.org

  9. 9 HingeHunt Fold Commons

    Residues bury at interfaces, and two domains may or may not "know" where each other sit (a first look at PAE).

    https://foldcommons.org/tools/hingehunt

Ages 15-18

Re-enter with the chemistry of bonds and the hydrophobic effect, then read real confidence numbers, quaternary structure, variants, isoforms, medicine and the blind tests that made prediction trustworthy.

  1. 10 ChemQuest Spark & Anvil

    Bonds, polarity, and the hydrophobic effect - the chemistry the older track re-enters on.

    https://sparkanvil.org

  2. 11 HelixQuest Spark & Anvil

    Gene sequence and variation -> protein -> evolution.

    https://sparkanvil.org

  3. 12 ShapeForge Spark & Anvil

    Predict local structure; hydrophobics bury; sickle cell is one changed letter. This rung hands off into the Fold Commons viewer.

    https://sparkanvil.org

  4. 13 NumberReader Fold Commons

    Read the real per-residue pLDDT numbers off a structure and say plainly: this is a prediction, not an experiment.

    https://foldcommons.org/tools/numberreader

  5. 14 GripChain Fold Commons

    Several chains assemble, and binding at one site changes another - quaternary structure and allostery.

    https://foldcommons.org/tools/gripchain

  6. 15 DomainCuts Fold Commons

    Domains and quantitative PAE; RMSD against the real PDB structure; a model omits cofactors and partners.

    https://foldcommons.org/tools/domaincuts

  7. 16 TolerancePaint Fold Commons

    Most variants are tolerated; AlphaMissense is a research tool, not a diagnosis.

    https://foldcommons.org/tools/tolerancepaint

  8. 17 SpliceSplit Fold Commons

    One gene can make several proteins - isoforms - each folding to its own shape.

    https://foldcommons.org/tools/splicesplit

  9. 18 PocketScout Fold Commons

    Structure -> pocket -> medicine; phenotype -> gene -> structure.

    https://foldcommons.org/tools/pocketscout

  10. 19 CASP, explained Fold Commons

    Why "prediction" became trustworthy - decades of CASP blind tests, and a Nobel Prize.

    https://foldcommons.org/tools/casptracker

Fold Commons — free, non-profit. Predictions, not experiments. Pathway per foldcommons.org/learn/pathway.