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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>LIVIA — Local Interaction Visualization and Analysis</title>
<style>
html { scrollbar-gutter: stable; } * { margin: 0; padding: 0; box-sizing: border-box; }
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.header h1 .livia { color: #2471A3; font-weight: 700; }
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.container { max-width: 1100px; margin: 0 auto; padding: 1.5rem; }
/* Paper banner */
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.paper-banner:hover .paper-arrow { transform: translateX(3px); }
@media (max-width: 600px) {
.paper-banner { flex-wrap: wrap; }
.paper-banner .paper-cite { flex-basis: 100%; }
}
/* Hero card */
.hero-card { background: white; border-radius: 14px; padding: 2rem 2.5rem; box-shadow: 0 2px 12px rgba(0,0,0,0.08); margin-bottom: 2rem; border: 2px solid transparent; transition: all 0.2s; text-decoration: none; color: #333; display: block; }
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.hero-card h2 { font-size: 1.5rem; color: #1a5276; margin-bottom: 0.4rem; }
.hero-card p { font-size: 0.92rem; color: #555; line-height: 1.5; }
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.footer a { color: #2471A3; text-decoration: none; }
@media (max-width: 1024px) {
.cards-grid { grid-template-columns: repeat(2, 1fr); }
}
@media (max-width: 600px) {
.cards-grid { grid-template-columns: 1fr; }
.hero-card { padding: 1.5rem; }
.hero-card h2 { font-size: 1.2rem; }
.bottom-row { flex-direction: column; }
}
</style>
</head>
<body>
<div class="header">
<div class="container">
<h1><span class="livia">LIVIA</span> — <span class="acro">L</span>ocal <span class="acro">I</span>nteraction <span class="acro">VI</span>sualization and <span class="acro">A</span>nalysis</h1>
<p class="subtitle">Analyze protein-protein interactions from structure predictions and generate visualization scripts</p>
<div class="header-links">
<a href="universal.html">Prediction Analysis</a>
<a href="flypredictome.html">FlyPredictome</a>
<a href="ortholog_predictome.html">Ortholog Interactome</a>
<a href="dimer.html">AFDB Dimer</a>
<a href="monomer.html">AFDB Monomer Subdomain</a>
<a href="tutorials.html">Tutorials</a>
<a href="about.html">About</a>
<a href="bookmarklet.html" style="background:#2471A3; color:white; border-color:#2471A3; font-weight:600;">Bookmarklet ★</a>
<a href="https://github.com/flyark/LIVIA" target="_blank">GitHub</a>
</div>
</div>
</div>
<div class="container">
<!-- Paper banner -->
<a class="paper-banner" href="https://doi.org/10.64898/2026.05.01.721633" target="_blank">
<span class="paper-icon">📄</span>
<span class="paper-cite">Kim & Perrimon (2026). LIVIA: a browser-based tool for assessing and visualizing predicted protein interactions. <em>bioRxiv</em>.</span>
<span class="paper-arrow">→</span>
</a>
<!-- Hero: Prediction Analysis -->
<a class="hero-card" href="universal.html">
<h2>Prediction Analysis</h2>
<p>Upload prediction files from AlphaFold-Multimer, AlphaFold3, ColabFold, Boltz-1/2, Chai-1, or OpenFold3. Calculate interface confidence metrics (iLIS, LIS, cLIS), view interactive PAE/LIS/cLIS maps, and generate visualization scripts.</p>
<span class="hero-cta">Launch Prediction Analysis →</span>
<div class="hero-hint">Supports any major structure prediction platform — no installation needed.</div>
</a>
<!-- Section divider -->
<div class="section-divider">Browse Precomputed Interactomes — <a href="https://www.flyrnai.org/tools/fly_predictome" target="_blank" style="color:#2471A3; font-weight:400;">FlyPredictome</a> · <a href="https://alphafold.ebi.ac.uk" target="_blank" style="color:#2471A3; font-weight:400;">AlphaFold DB</a></div>
<!-- Four small cards -->
<div class="cards-grid">
<a class="small-card" href="flypredictome.html">
<h3>FlyPredictome</h3>
<p>Search <em>Drosophila</em> protein interactions from FlyPredictome predictions (Kim et al., 2026).</p>
<div class="examples">e.g., Akt1–foxo, Dl–N, Dsh–Axn</div>
</a>
<a class="small-card" href="ortholog_predictome.html">
<h3>Ortholog Interactome</h3>
<p>Search human kinase–TF interactions from ortholog predictions (Kim et al., 2025).</p>
<div class="examples">e.g., TP53, CDK2, AKT1, BRAF</div>
</a>
<a class="small-card" href="dimer.html">
<h3>AFDB Dimer</h3>
<p>Fetch dimer predictions from the AlphaFold Protein Structure Database (Han et al., 2026).</p>
<div class="examples">e.g., Fiber protein 2, pp71</div>
</a>
<a class="small-card" href="monomer.html">
<h3>AFDB Monomer Subdomain</h3>
<p>Analyze intramolecular domain interactions in AlphaFold monomer predictions.</p>
<div class="examples">e.g., Haspin (Q8TF76), SCN9A (Q15858)</div>
</a>
</div>
<!-- Tutorials + Guide + GitHub -->
<div class="bottom-row">
<a class="bottom-link" href="tutorials.html">
<h4>Tutorials</h4>
<p>Visual walkthroughs for each tool — learn by example.</p>
</a>
<a class="bottom-link" href="about.html">
<h4>About</h4>
<p>Metric definitions, color schemes, and references.</p>
</a>
<a class="bottom-link" href="https://github.com/flyark/LIVIA" target="_blank">
<h4>GitHub</h4>
<p>Source code, documentation, and issue tracker.</p>
</a>
</div>
</div>
<div style="max-width:1100px; margin:0 auto; padding:0 1.5rem 1rem;">
<div style="background:#f8f9fa; border-radius:8px; padding:0.8rem 1.2rem; font-size:0.78rem; color:#888; line-height:1.6;">
<strong style="color:#555;">Browser:</strong> Tested on Chrome and Safari (macOS/iOS). All analysis runs locally in your browser — no data leaves your device.
<br>
<strong style="color:#555;">Note:</strong> Each prediction platform (AlphaFold3, ColabFold, Boltz, Chai-1, etc.) may produce different confidence calibrations. The iLIS ≥ 0.223 threshold was established using ColabFold/AlphaFold-Multimer predictions. Other platforms may require adjusted thresholds.
</div>
</div>
<div class="footer">
<a href="https://github.com/flyark/LIVIA" target="_blank">LIVIA GitHub</a> · <a href="https://github.com/flyark/AFM-LIS" target="_blank">AFM-LIS GitHub</a>
<br>
<a href="https://doi.org/10.64898/2026.05.01.721633" target="_blank">Kim & Perrimon (2026)</a>
<br>
Ah-Ram Kim · Harvard Medical School
</div>
<script data-goatcounter="https://livia.goatcounter.com/count"
async src="//gc.zgo.at/count.js"></script>
</body>
</html>