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3-D protein structure viewer for JBrowse 2, linked residue by residue to the genome.","maintainers":[{"name":"cmdcolin","email":"colin.diesh@gmail.com"}],"readme":"# jbrowse-plugin-protein3d\n\nA 3-D protein structure viewer for JBrowse 2, linked residue by residue to the\ngenome.\n\n![TP53 beside PDB 1TUP, p53's core domain bound to DNA, with the R248 hotspot selected](https://raw.githubusercontent.com/GMOD/jbrowse-plugin-protein3d/readme-figure/readme.png)\n\nTP53 beside PDB 1TUP, p53's core domain bound to DNA. R248, a cancer hotspot, is\nselected in magenta on the structure, and its codon is marked on the gene.\n[Open this session](https://jbrowse.org/code/jb2/main/?config=test_data/protein3d_config.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22ProteinView%22%2C%22structures%22%3A%5B%7B%22pdbId%22%3A%221TUP%22%2C%22initialResidues%22%3A%7B%22start%22%3A248%2C%22end%22%3A248%7D%7D%5D%2C%22transcriptId%22%3A%22NM_000546.6%22%2C%22sideBySide%22%3Atrue%2C%22zoomToBaseLevel%22%3Afalse%2C%22colorScheme%22%3A%22mapped-chain%22%2C%22connectedView%22%3A%7B%22assembly%22%3A%22hg38%22%2C%22loc%22%3A%22chr17%3A7%2C673%2C700-7%2C674%2C700%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22hg38-ncbiRefSeq%22%2C%22geneGlyphMode%22%3A%22longestCoding%22%7D%2C%22clinvar_ncbi_hg38%22%5D%7D%7D%5D%7D).\nCI re-renders the figure from `main` every hour\n([scripts/readme-figure.mjs](scripts/readme-figure.mjs)).\n\nRight-click a gene and choose to open its protein structure. The plugin looks up\nthe AlphaFold model through UniProt, lists the experimental PDB entries SIFTS\nmaps to that UniProt entry, and can search Foldseek for related structures. It\naligns each structure to the transcript's translation, so hovering a residue\nhighlights its codon and hovering a codon highlights its residue.\n\n## Try it\n\nThe [protein browser](https://staging.genomes.jbrowse.org/protein-browser/)\ntakes a gene name and opens it in JBrowse with its structure linked to the\ngenome. The plugin is also installed by default on\n[genomes.jbrowse.org](https://genomes.jbrowse.org), so it works for any species\nthere.\n\n## Documentation\n\nUsing the plugin:\n\n- Tutorials on jbrowse.org:\n  [TP53 from prediction to crystal](https://jbrowse.org/jb2/docs/tutorials/tp53_structures/)\n  opens an AlphaFold model and two crystal structures superposed beside the\n  gene, and reads the R248 hotspot back to its codon;\n  [Proteins on genomes.jbrowse.org](https://jbrowse.org/jb2/docs/tutorials/genomes_proteins/)\n  launches a structure and an MSA from any gene's right-click menu.\n- [Demos](docs/demos.md): structures that are easy to map wrong, each one link\n  away — a peptide bound to a larger partner, a protein bound to DNA, a receptor\n  with another protein fused into it, a phosphorylated residue, and a\n  mitochondrial protein.\n- [Your own structures](docs/your-own-structures.md): opening a model you folded\n  yourself (ColabFold, AlphaFold 3, Boltz…) instead of the AlphaFold DB one,\n  from a file, a URL or a generated link per gene, and which features carry\n  over.\n\nLinking and embedding:\n\n- [Launching from a URL or code](docs/launching.md): worked session-spec links,\n  the short `uniprotId`/`pdbId` + `transcriptId` form, several structures in one\n  view, and the `LaunchView-ProteinView` extension point.\n- [Launch parameters](docs/launch-parameters.md): every argument, the\n  `connectedView` settings, and the transcript `feature` shape.\n- [Session snapshots](docs/session-snapshots.md): the saved view's shape, the\n  structure shorthands, and which chain maps.\n\nHow it works, for someone extending the plugin or checking what a number on\nscreen means:\n\n- [Genome to structure alignment](docs/genome-to-structure-alignment.md): why\n  the plugin aligns the transcript's translation to the structure on the fly,\n  the precedent for that in SIFTS and G2S, how it picks the chain and isoform,\n  and what sequence alignment cannot decide.\n- [UniProt feature tracks](docs/uniprot-feature-tracks.md): where the accession\n  and the UniProt-to-structure offset come from for AlphaFold models, PDB\n  entries and your own models.\n- [The secret sauce](docs/secret-sauce.md): one variable drawn with one scale in\n  the 3D view, the alignment strip and the genome track, and the ideas that\n  build on it, such as painting any genome track onto the structure.\n- [Residue numbering](docs/residue-numbering.md): how a paper's R248 becomes\n  position 154 in the file, `label_seq_id` 155 for Mol\\*, and the codon on\n  chr17, and how a session spec names a residue the literature's way.\n\nWorking on the plugin:\n\n- [DEVELOPERS.md](DEVELOPERS.md): running it locally and publishing.\n- [Testing](docs/testing.md): the unit, e2e, documentation and demo checks.\n- [Host compatibility](docs/host-compatibility.md): keeping the published bundle\n  working on JBrowse releases years old.\n- [Live checks](docs/live-checks.md): serving a local build to a session on\n  jbrowse.org.\n\n## Publication\n\nIf you find this tool useful please cite our work\n\nDiesh, C., Stevens, G., Bridge, C., Hogue, G., Buels, R., Cain, S., Stein, L., &\nHolmes, I. (2026). Proteins in the Genome Browser: Integration of Phylogenies,\nAlignments, and Structures With Nucleotide-level Evidence in JBrowse 2. Journal\nof Molecular Biology, 169645. https://doi.org/10.1016/j.jmb.2026.169645\n\nSee also https://github.com/GMOD/proteinbrowser for overview\n","readmeFilename":"README.md"}