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<!DOCTYPE html>
<html lang="en" class="scroll-smooth">
<head>
<meta charset="UTF-8" />
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<title>Boltz2 Notebook | AI Biomolecular Structure Prediction</title>
<meta name="description" content="Boltz2 Notebook is a Colab-first interface for advanced biomolecular structure prediction, protein-ligand affinity analysis, multi-entity modeling, and batch screening powered by Boltz2." />
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</head>
<body>
<div class="site-shell">
<header class="topbar">
<div class="container nav-wrap">
<a class="brand" href="#hero" aria-label="Boltz2 Notebook home">
<img src="assets/boltz2-mark.svg" alt="Boltz2 Notebook logo" class="brand-mark" />
<div>
<div class="brand-name">Boltz2 Notebook</div>
<div class="brand-subtitle">Colab-first advanced biomolecular modeling</div>
</div>
</a>
<button class="nav-toggle" id="navToggle" aria-expanded="false" aria-controls="navMenu">
<span></span><span></span><span></span>
</button>
<nav class="nav-menu" id="navMenu">
<a href="#features">Features</a>
<!-- <a href="#protein-viewer">Viewer</a> -->
<a href="#workflow">Workflow</a>
<a href="#versions">Versions</a>
<a href="#batch">Batch</a>
<a href="docs/use-cases.html">Use Cases</a>
<a href="docs/faq.html">FAQ</a>
<a href="#citation">Cite</a>
<a href="https://github.com/AtharvaTilewale/boltz2-notebook" target="_blank" rel="noreferrer">GitHub</a>
</nav>
</div>
</header>
<main>
<section class="hero" id="hero">
<div class="hero-noise"></div>
<!-- <div id="bgViewer" class="hero-bg-viewer"></div> -->
<div class="container hero-grid">
<div class="hero-copy reveal">
<div class="eyebrow">AI biomolecular structure prediction</div>
<h1>From sequence to structure, affinity, and screening — in one polished notebook workflow.</h1>
<p class="hero-text">
Boltz2 Notebook packages Boltz2 into a guided, research-ready interface for protein structure prediction,
protein–ligand modeling, DNA/RNA-enabled complexes, confidence analysis, and batch-scale runs without local GPU setup.
</p>
<div class="hero-actions">
<a class="btn btn-primary" href="https://colab.research.google.com/github/AtharvaTilewale/boltz2-notebook/blob/main/Boltz2.ipynb" target="_blank" rel="noreferrer">Launch Main Notebook</a>
<a class="btn btn-secondary" href="https://github.com/AtharvaTilewale/boltz2-notebook" target="_blank" rel="noreferrer">View Repository</a>
</div>
<div class="badge-row">
<span class="badge">Python 3.10</span>
<span class="badge">CUDA-enabled</span>
<span class="badge">Google Colab</span>
<span class="badge">MIT License</span>
</div>
</div>
<div class="hero-panel reveal delay-1">
<div class="panel-top">
<span class="status-pill live">Production-ready workflow</span>
<span class="status-pill">No local install</span>
</div>
<div class="terminal-card">
<div class="terminal-head">
<span></span><span></span><span></span>
</div>
<div class="terminal-body">
<div class="code-line muted"># Example job definition</div>
<div class="code-line"><span class="key">protein_sequence</span>: <span class="value">MSEQNNTEMT...</span></div>
<div class="code-line"><span class="key">ligand_smiles</span>: <span class="value">CCO</span></div>
<div class="code-line"><span class="key">binder</span>: <span class="value">B</span></div>
<div class="code-line"><span class="key">msa_mode</span>: <span class="value">server</span></div>
<div class="code-line"><span class="key">template_file</span>: <span class="value">template.pdb</span></div>
<div class="code-spacer"></div>
<div class="metric-grid">
<div class="metric-card">
<span>Core outputs</span>
<strong>Structures + confidence</strong>
</div>
<div class="metric-card">
<span>Affinity support</span>
<strong>Prediction + ranking</strong>
</div>
<div class="metric-card">
<span>Typical runtime</span>
<strong>2–10 min on T4</strong>
</div>
<div class="metric-card">
<span>Best for</span>
<strong>Research & screening</strong>
</div>
</div>
</div>
</div>
</div>
</div>
</section>
<section class="strip">
<div class="container stats-grid reveal">
<div class="stat-card">
<strong>3</strong>
<span>Launch paths</span>
<p>V1 stable, V2 beta, and Batch.</p>
</div>
<div class="stat-card">
<strong>4</strong>
<span>Batch input modes</span>
<p>CSV, FASTA, YAML ZIP, and YAML folder workflows.</p>
</div>
<div class="stat-card">
<strong>7-step</strong>
<span>Batch run system</span>
<p>From workspace bootstrap to archival export.</p>
</div>
<div class="stat-card">
<strong>Zero-install</strong>
<span>Colab-first delivery</span>
<p>Designed to remove local GPU and CLI friction.</p>
</div>
</div>
</section>
<section class="section" id="features">
<div class="container">
<div class="section-heading reveal">
<span class="kicker">Why this notebook exists</span>
<h2>Research-grade modeling without the usual setup overhead.</h2>
<p>
The repository combines notebook UX, Python utilities, release tracking, and batch orchestration into one
coherent entry point for structure prediction and interaction analysis.
</p>
</div>
<div class="feature-grid">
<article class="feature-card reveal">
<div class="feature-icon">01</div>
<h3>Protein & complex prediction</h3>
<p>Run single-chain, multi-chain, and ligand-bound predictions through a guided notebook workflow.</p>
</article>
<article class="feature-card reveal delay-1">
<div class="feature-icon">02</div>
<h3>Affinity-aware analysis</h3>
<p>Surface confidence metrics, predicted aligned error, and affinity-oriented outputs in the same workflow.</p>
</article>
<article class="feature-card reveal delay-2">
<div class="feature-icon">03</div>
<h3>Advanced multi-entity support</h3>
<p>V2 expands into DNA, RNA, PTMs, covalent chemistry, contact conditioning, and template-guided jobs.</p>
</article>
<article class="feature-card reveal">
<div class="feature-icon">04</div>
<h3>Batch screening</h3>
<p>Queue many jobs from structured inputs and rank results for large-scale exploration and prioritization.</p>
</article>
<article class="feature-card reveal delay-1">
<div class="feature-icon">05</div>
<h3>Interactive outputs</h3>
<p>Designed around visualization, analysis summaries, exportable artifacts, and reproducible notebook usage.</p>
</article>
<article class="feature-card reveal delay-2">
<div class="feature-icon">06</div>
<h3>Built for accessibility</h3>
<p>Use free Colab GPU resources instead of managing a local CUDA installation and runtime configuration.</p>
</article>
</div>
</div>
</section>
<section class="section alt" id="workflow">
<div class="container">
<div class="section-heading narrow reveal">
<span class="kicker">End-to-end flow</span>
<h2>A clear path from biomolecular input to exported results.</h2>
</div>
<div class="vertical-stepper reveal">
<div class="stepper-step">
<div class="step-marker">01</div>
<div class="step-content">
<h3>Setup</h3>
<p>Initialize the notebook environment, install dependencies, and configure workspace directories.</p>
</div>
</div>
<div class="stepper-step">
<div class="step-marker">02</div>
<div class="step-content">
<h3>Build inputs</h3>
<p>Provide protein, ligand, DNA/RNA, MSA, and template details through structured parameters.</p>
</div>
</div>
<div class="stepper-step">
<div class="step-marker">03</div>
<div class="step-content">
<h3>Run Boltz2</h3>
<p>Generate MSAs, launch predictions, recycle structures, and produce PDB or CIF outputs.</p>
</div>
</div>
<div class="stepper-step">
<div class="step-marker">04</div>
<div class="step-content">
<h3>Analyze</h3>
<p>Inspect pLDDT, PAE, confidence, and affinity-linked metrics to assess output quality.</p>
</div>
</div>
<div class="stepper-step">
<div class="step-marker">05</div>
<div class="step-content">
<h3>Visualize</h3>
<p>Review structures interactively and compare candidate predictions for downstream interpretation.</p>
</div>
</div>
<div class="stepper-step last">
<div class="step-marker">06</div>
<div class="step-content">
<h3>Export</h3>
<p>Download zipped artifacts or save runs to Drive for sharing, reuse, and traceability.</p>
</div>
</div>
</div>
</div>
</section>
<section class="section alt" id="usecases-intro">
<div class="container">
<div class="section-heading narrow reveal">
<span class="kicker">Real-world applications</span>
<h2>How teams use Boltz2 Notebook.</h2>
</div>
<div class="usecases-intro-grid reveal">
<div class="usecase-mini-card">
<h3>Drug Discovery</h3>
<p>Predict protein-ligand binding poses and affinity scores to screen compounds without wet lab costs.</p>
</div>
<div class="usecase-mini-card">
<h3>Enzyme Engineering</h3>
<p>Design multi-chain enzyme complexes with template guidance and constraint conditioning for better function.</p>
</div>
<div class="usecase-mini-card">
<h3>Structure Validation</h3>
<p>Rapidly validate experimental structures against predictions and compare confidence metrics (pLDDT, PAE).</p>
</div>
</div>
<div class="reveal" style="text-align: center; margin-top: 2rem;">
<a href="docs/use-cases.html" class="btn btn-secondary">View detailed protocols →</a>
</div>
</div>
</section>
<section class="section" id="versions">
<div class="container">
<div class="section-heading reveal">
<span class="kicker">Notebook lineup</span>
<h2>Choose the right surface for the job.</h2>
</div>
<div class="version-grid">
<article class="version-card featured reveal">
<div class="card-head">
<div>
<span class="label">Main entry (Stable)</span>
<h3>Main Notebook (V1.0.0)</h3>
</div>
<span class="tag">Recommended</span>
</div>
<p>General-use interface for structure prediction, ligand binding, affinity analysis, confidence inspection, and export.</p>
<ul>
<li>Multi-chain proteins</li>
<li>Protein–ligand support</li>
<li>Affinity analysis and visualization</li>
</ul>
<a class="text-link" href="https://colab.research.google.com/github/AtharvaTilewale/boltz2-notebook/blob/main/Boltz2.ipynb" target="_blank" rel="noreferrer">Open notebook →</a>
</article>
<article class="version-card reveal delay-2">
<div class="card-head">
<div>
<span class="label">Beta</span>
<h3>V2.0.0</h3>
</div>
<span class="tag">Advanced</span>
</div>
<p>Extended modeling stack for more complex jobs, including constraints, templates, DNA/RNA, and PTMs.</p>
<ul>
<li>DNA/RNA support</li>
<li>Custom MSA & templates</li>
<li>Covalent and contact constraints</li>
</ul>
<a class="text-link" href="https://colab.research.google.com/github/AtharvaTilewale/boltz2-notebook/blob/main/colab/v2/Boltz2_V2.0.0_beta.ipynb" target="_blank" rel="noreferrer">Open V2 beta →</a>
</article>
<article class="version-card reveal delay-1">
<div class="card-head">
<div>
<span class="label">Experimental</span>
<h3>Batch V1.0.0</h3>
</div>
<span class="tag neutral">Batch</span>
</div>
<p>Designed for high-throughput screening and structured job management.</p>
<ul>
<li>Multiple input modes: CSV, FASTA, YAML ZIP/folder</li>
<li>Manifest-driven batch execution</li>
<li>Input validation and run profiles</li>
</ul>
<a class="text-link" href="https://colab.research.google.com/github/AtharvaTilewale/boltz2-notebook/blob/main/batch/Boltz2_Batch_v1_beta.ipynb" target="_blank" rel="noreferrer">Open Batch Notebook →</a>
</article>
</div>
<div class="comparison-table reveal">
<div class="table-row table-head">
<span>Capability</span><span>V1</span><span>V2</span><span>Batch</span>
</div>
<div class="table-row"><span>Single protein prediction</span><span>✓</span><span>✓</span><span>✓</span></div>
<div class="table-row"><span>Protein–ligand binding</span><span>✓</span><span>✓</span><span>✓</span></div>
<div class="table-row"><span>DNA / RNA support</span><span>—</span><span>✓</span><span>—</span></div>
<div class="table-row"><span>Templates & custom MSA</span><span>Partial</span><span>✓</span><span>✓</span></div>
<div class="table-row"><span>PTMs / constraints / covalent links</span><span>—</span><span>✓</span><span>—</span></div>
<div class="table-row"><span>Batch processing</span><span>—</span><span>—</span><span>✓</span></div>
</div>
</div>
</section>
<!-- <section class="section" id="protein-viewer">
<div class="container">
<div class="section-heading narrow reveal">
<span class="kicker">Interactive visualization</span>
<h2>Explore predicted structures in real-time.</h2>
<p>3D protein viewer powered by 3Dmol.js with full rotation, zoom, and analysis controls. Load any predicted structure or PDB file.</p>
</div>
<div class="viewer-container reveal">
<div class="viewer-grid">
<div class="viewer-panel">
<div id="viewer" class="protein-viewer"></div>
<div class="viewer-controls">
<button class="control-btn" id="resetView" title="Reset view">↻ Reset</button>
<button class="control-btn" id="cartoonView" title="Cartoon representation">🎬 Cartoon</button>
<button class="control-btn" id="stickView" title="Stick representation">🔗 Stick</button>
<button class="control-btn" id="sphereView" title="Space-filling">● Sphere</button>
</div>
</div>
<div class="viewer-info">
<div class="info-card">
<h3>Sample Protein: Hemoglobin</h3>
<p>A classic multi-chain complex showing how Boltz2 handles protein–protein interactions and confidence-linked coloring.</p>
<div class="info-section">
<strong>Controls</strong>
<ul class="control-list">
<li><strong>Left drag:</strong> Rotate structure</li>
<li><strong>Right drag:</strong> Pan view</li>
<li><strong>Scroll:</strong> Zoom in/out</li>
<li><strong>Buttons:</strong> Switch representations</li>
</ul>
</div>
<div class="info-section">
<strong>What you're seeing</strong>
<p>Hemoglobin is colored by chain (A, B, C, D). Each representation reveals different structural details—cartoon for secondary structure, stick for atomic detail, and sphere for van der Waals surfaces.</p>
</div>
<div class="info-section">
<strong>Your predictions</strong>
<p>Load your Boltz2-predicted structures the same way. Use the notebook to export PDB files, then drop them here to visualize confidence metrics and binding interfaces.</p>
</div>
<a href="https://colab.research.google.com/github/AtharvaTilewale/boltz2-notebook/blob/main/Boltz2.ipynb" class="btn btn-primary" target="_blank" rel="noreferrer">Start a prediction</a>
</div>
</div>
</div>
</div>
</div>
</section> -->
<section class="section alt" id="batch">
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<div class="reveal">
<div class="section-heading left">
<span class="kicker">Batch mode</span>
<h2>Designed for high-throughput screening and structured job management.</h2>
<p>
The batch notebook wraps multiple jobs into a manifest-driven system with preflight validation,
configurable run profiles, result ranking, and exportable archives.
</p>
</div>
<div class="pill-list">
<span>CSV input</span>
<span>FASTA input</span>
<span>YAML ZIP bundles</span>
<span>YAML folders</span>
<span>Fast / Balanced / Scientific profiles</span>
<span>Skip-complete / retry-failed options</span>
</div>
</div>
<div class="batch-card reveal delay-1">
<div class="mini-grid">
<div>
<h3>Input builder</h3>
<p>Validate job specifications before expensive runs start.</p>
</div>
<div>
<h3>Execution engine</h3>
<p>Launch, resume, queue, and monitor multiple jobs in one notebook flow.</p>
</div>
<div>
<h3>Ranking layer</h3>
<p>Sort candidates by affinity probability, confidence, pLDDT, pTM, and related metrics.</p>
</div>
<div>
<h3>Archival export</h3>
<p>Bundle predictions, manifests, logs, and outputs into a shareable ZIP artifact.</p>
</div>
</div>
<a class="btn btn-secondary full" href="https://colab.research.google.com/github/AtharvaTilewale/boltz2-notebook/blob/main/batch/Boltz2_Batch_v1_beta.ipynb" target="_blank" rel="noreferrer">Launch Batch Notebook</a>
</div>
</div>
</div>
</section>
<section class="section">
<div class="container">
<div class="section-heading narrow reveal">
<span class="kicker">Release highlights</span>
<h2>What changed across versions.</h2>
</div>
<div class="release-grid">
<article class="release-card reveal">
<span class="release-version">v2.0.0</span>
<h3>Advanced modeling stack</h3>
<p>Template upload, explicit chain mapping, covalent bonds, pocket conditioning, contact conditioning, modified residues, custom MSA, DNA/RNA support, and cyclic polymer options.</p>
</article>
<article class="release-card reveal delay-1">
<span class="release-version">v1.0.0</span>
<h3>Public notebook foundation</h3>
<p>Initial release with protein–ligand prediction, affinity workflow, visualization, Drive export, and ZIP output packaging.</p>
</article>
<article class="release-card reveal delay-2">
<span class="release-version">Batch v1</span>
<h3>Automation layer</h3>
<p>Multiple predictions, manifest-based execution, ranking, and large-scale run organization for practical screening.</p>
</article>
</div>
</div>
</section>
<section class="section faq-section" id="faq">
<div class="container">
<div class="section-heading narrow reveal">
<span class="kicker">FAQ</span>
<h2>Start with the most important questions, then open the full FAQ page.</h2>
<p>
These answers reflect the current notebook lineup, the batch guide, and the release notes so visitors can
quickly find the right workflow.
</p>
</div>
<div class="faq-list reveal">
<details>
<summary>Do I need a local GPU or CUDA installation?</summary>
<p>No. The notebooks are designed around Google Colab, so you can run the main workflow without managing a local CUDA setup.</p>
</details>
<details>
<summary>Which notebook should I start with?</summary>
<p>Use the main notebook for general predictions, V2 for advanced modeling, and Batch when you need to screen many jobs at once.</p>
</details>
<details>
<summary>What kinds of inputs are supported?</summary>
<p>The repository supports proteins, ligands, templates, custom MSAs, DNA/RNA in V2, and CSV/FASTA/YAML batch manifests.</p>
</details>
<details>
<summary>What outputs can I expect?</summary>
<p>Predicted structures, confidence metrics such as pLDDT and PAE, affinity-oriented outputs, visualizations, logs, and exportable ZIP bundles.</p>
</details>
</div>
<div class="faq-cta reveal delay-1">
<a class="btn btn-primary" href="docs/faq.html#faq-search">Explore all FAQs</a>
<a class="btn btn-secondary" href="docs/use-cases.html">View Use-Case Protocols</a>
</div>
</div>
</section>
<section class="section alt" id="citation">
<div class="container">
<div class="section-heading narrow reveal">
<span class="kicker">Cite this project</span>
<h2>Please cite Boltz2 Notebook in publications and reports</h2>
<p>Use the following citation formats when referring to the notebook or repository in academic work.</p>
</div>
<div class="citation-grid reveal">
<div class="citation-card">
<h3>Recommended citation</h3>
<div style="display:flex; gap:0.5rem; align-items:center; margin-bottom:0.5rem;">
<label for="citationFormatSelect" style="font-weight:600;">Format:</label>
<select id="citationFormatSelect" class="text-input">
<option value="apa">APA (default)</option>
<option value="mla">MLA</option>
<option value="ieee">IEEE</option>
<option value="chicago">Chicago</option>
</select>
</div>
<pre class="citation-display"><code id="citationText">Tilewale, A., & Patel, D. (2026). Boltz2-Notebook: A streamlined Colab-based pipeline for biomolecular structure prediction and binding affinity analysis using the Boltz2 deep learning model. https://doi.org/10.5281/zenodo.21850102</code></pre>
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<h3>BibTeX</h3>
<div class="code-meta" style="display:flex; gap:0.5rem; align-items:center; margin-bottom:0.5rem;">
</div>
<pre class="bibtex-block"><code id="bibtexBlock">@misc{tilewale2026boltz2,
author = {Tilewale, Atharva and Patel, Dhaval},
title = {Boltz2-Notebook: A streamlined Colab-based pipeline for biomolecular structure prediction and binding affinity analysis using the Boltz2 deep learning model},
year = {2026},
howpublished = {\url{https://github.com/AtharvaTilewale/boltz2-notebook}},
doi = {10.5281/zenodo.21850102}
}</code></pre>
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