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Drybench
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Drybench Cell.

Follow how a human cell turns a gene into a working protein through an interactive structure tour. Each step uses a deposited Protein Data Bank structure and links to its primary paper.

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Example data: Step 5: the ribosome. PDB 6Y0G (CC0 1.0). Bhaskar V et al. Cell Rep 2020;31:107473.

  • Free to use
  • Runs in your browser
  • Transparent methods

Illustration · Explore the real workspace below

See the tools at work.

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stills 50 to 130 KB each; the 3D view about 1.5 MB, on request

What you can do with it

  • 8-step guided tour

    Chromatin, transcription, splicing, export, translation, the exit tunnel, folding and haemoglobin, in order, with one colour scheme throughout.

  • Real human structures

    Eight PDB entries checked against the RCSB PDB, Europe PMC and UniProt, each shown with its method, resolution and primary paper.

  • 3D plus Blender stills

    A still rendered in Blender appears at once; the Mol* 3D view loads when you ask and keeps the same colours, cutaway and camera.

  • Sizes on one scale

    All eight structures on one nanometre scale, so a nucleosome can be set against a ribosome.

  • Measured from the structures

    Sizes and counts in the text were measured from the deposited coordinates by a reproducible pipeline.

  • What you are looking at

    Each step names the parts on screen against a colour key, and the 3D labels and tooltips use the same words.

  • An address for every step

    Each step has its own address, so a shared link opens the tour on that step's text and picture.

  • The whole tour as text

    All eight steps as plain text, for reading straight through, printing or a screen reader.

See the evidence behind the answer.

Explore the methods and sources behind the tools.

Read the methods
Where every panel's data comes from
  • RCSB Protein Data Bank
    RCSB Protein Data BankCC0 1.0

    Atomic coordinates (BinaryCIF, trimmed by the pipeline) and entry metadata for all eight structures

    PDB entries 3AFA, 8XSO, 6QDV, 7ZNK, 6Y0G, 6OLE, 7TUB and 2DN1; each step cites its primary paper

  • UniProt
    UniProtCC BY 4.0

    Protein names, lengths and function notes behind the text; accessions for the protein explorer links

    The UniProt Consortium. UniProt: the Universal Protein Knowledgebase in 2025. Nucleic Acids Res 2025;53:D609-D617.

  • Europe PMC
    Europe PMCEMBL-EBI terms of use (no added restrictions)

    Checking each citation's title, authors, year and DOI, and the background abstracts behind a few facts (PMIDs 21195232, 24459735, 24196718 and 20118940)

  • RNAcentral
    RNAcentralCC0 1.0

    Identifying the tRNA sequence in PDB 6Y0G as Escherichia coli tRNA-Phe (URS00005AA258)

  • PDB-101 Molecule of the Month
    PDB-101 Molecule of the MonthArticles © RCSB PDB and authors; background reading only, no text reused

    Background on nucleosomes, RNA polymerase, spliceosomes, the nuclear pore, ribosomes, tRNA, chaperones and haemoglobin

    David S. Goodsell and the RCSB PDB

  • Mol* 5.11.0
    Mol* 5.11.0MIT

    The 3D viewer and MolViewSpec scenes

    Sehnal D et al. Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Res 2021;49:W431-W437.

  • Blender 5.2 (bpy 5.2.2)
    Blender 5.2 (bpy 5.2.2)GPL-3.0-or-later for Blender binaries such as bpy (source GPL-2.0-or-later); build-time tool only, no code shipped

    Rendering the step stills (Cycles, headless); the outputs are not covered by the GPL

    Blender Foundation

  • Molecular Nodes
    Molecular NodesGPL-3.0-or-later; build-time tool only, no code shipped

    Loading and styling the structures in Blender for the stills

    Brady Johnston

  • Biotite
    BiotiteBSD-3-Clause

    Reading, measuring and trimming the structure files in the build pipeline

  • NumPy and SciPy
    NumPy and SciPyBSD-3-Clause

    Measuring sizes (convex hull) and camera axes in the build pipeline

Where it runs and what it sends

This app declares no external public data hosts.

Anything in the address bar before the # (a search, a SMILES, an accession or a step) is sent to this site's host when a page loads or a link is opened; anything after the # is not sent.

Not used, by licence:

  • AlphaFold 3 outputs. Their terms allow non-commercial use only; every structure in the tour is experimental.
  • DrugBank. Its licence is non-commercial; drug names come from the PDB entries and the primary papers.

Third-party notices

Built for research and education. The tools have not been validated for regulated use. Read the regulatory position

Make your next step a practical one.

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