Protein Design Subway Map
Start with structure prediction and de novo protein design. Choose another workflow to explore its methods, documentation and sources.
Start with structure prediction and de novo protein design. Choose another workflow to explore its methods, documentation and sources.
Protein design today means stitching together a dozen-plus tools — backbone generators, sequence designers, structure predictors, dockers, developability screens. This map treats that ecosystem like a subway system (Inspired by London Underground): stations are tools, colored lines are common workflows, and tracks connect them through gates.
Gates describe the data transfers and analysis steps between tools. Only explicitly sourced criteria are shown: published protocol filters and author interpretation guidance are labelled separately. A score or a track is not proof of binding. Regular stations belong to a single workflow. Double-ringed stations are transfer stations — tools shared across multiple workflows.
The dashed tracks are feedback loops: when a design needs revision, work goes back upstream to be redone. They run in their own lanes below the tracks, and the Tracks switch in the bar shows the main gates, the loops, or both.
The map opens with De Novo Protein Design only. Select additional lines to expand the view, or choose All workflows for the complete catalogue. Reset returns to protein design. Pick a line up top to filter workflows, or click any station or track to see inputs, outputs and any sourced criteria. Open the small Evidence controls for the exact source and scope. Use search (top right) to jump straight to a station, ↺ to reset the view, and ↓ to export what you're currently looking at as a PNG.
Data corrections from Srikanth Lingappa’s Protein Design Subway Map (4bec627), incorporated 2026-09-19. Verify tool-specific metrics and thresholds against the linked papers and documentation.
Criteria review: 13 October 2026. Paper/preprint references are separate from author documentation. No unsourced acceptance cutoffs have been added. Displayed settings are illustrative unless explicitly stated otherwise.
A reference guide to published tools. Station links lead to papers and official software. Metric interpretations depend on their stated context; computational scores are not experimental measurements.
Bibliography checked 13 October 2026. Software citations must match the version actually used. Method results and map performance claims are not revalidated by this check.
The visual language is borrowed from Harry Beck's 1933 London Underground map.