Pinned Post
May 13
🚀 New tool out! LIVIA (Local Interaction Visualization and Analysis) — a browser-based tool for assessing and visualizing predicted protein-protein interactions.
Drop in a prediction from AlphaFold-Multimer, AF3, ColabFold, Boltz-1/2, Chai-1, or OpenFold3 (ZIP or folder, auto-detected) and LIVIA answers the two questions you actually care about:
▸ Do these proteins interact?
▸ Which residues form the interface?
What you get:
▸ Interface confidence scores — iLIS (our local metric), ipSAE, actifpTM, ipTM
▸ Interaction interface heatmaps (PAE, LIS, cLIS)
▸ Sequence viewer linear & circular contact maps highlighting Local Interaction Residues (LIR) and contact LIR (cLIR)
▸ Embedded Mol* 3D viewer
▸ Downloadable ChimeraX & PyMOL scripts
Also fetches dimers directly from the AlphaFold Database — adding the interface annotations AFDB doesn't provide.
Everything runs locally in your browser. No install, no upload.
LIVIA started as a personal tool — I built it with Claude Code and used it to make every structure figure in our FlyPredictome preprint (Kim et al., 2026). (Claude Code is truly insane...) Along the way I realized it could be useful for others, too.
If you have a favorite color palette for structure visualization, please let me know — happy to add it as a preset 🎨
🔗 LIVIA tool: flyark.github.io/LIVIA
🐍 iLIS / batch CLI: github.com/flyark/AFM-LIS
📄 LIVIA preprint: biorxiv.org/content/10.64898…
📄 FlyPredictome preprint: biorxiv.org/content/10.64898…
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