Getting Started

Welcome to LatticeZero! This guide walks you through your first project — from uploading a receptor to scoring ligands — in under 10 minutes.

Prerequisites

• A modern browser with WebGPU support (Chrome 113+, Edge 113+, Firefox Nightly)
• A receptor PDB file (or use one of our built-in demo targets)
• Ligand files in SDF or MOL2 format

Note: LatticeZero runs entirely in your browser using WebGPU. No software installation, no cloud compute costs.

Step 1: Create an Account

1. Navigate to app.latticezero.com
2. Click Sign Up and fill in your details
3. Verify your email address
4. Log in to reach your Dashboard

Step 2: Create a Project

Projects organize your targets and scoring runs.

1. Click Projects in the sidebar
2. Click + New Project
3. Give it a name (e.g., "My First Docking Study")
4. Optionally add a description
5. Click Create

Step 3: Prepare Your Target

Before scoring ligands, you need a prepared receptor with a defined binding pocket.

Option A: Use a Demo Target

The fastest way to get started:

1. Go to Target Library in the sidebar
2. Browse the pre-prepared targets (ACE, EGFR, CDK2, HSP90, etc.)
3. Click Use Target to add it to your project

Option B: Upload Your Own PDB

1. In your project, click Target Prep
2. Upload your PDB file (or enter a PDB ID to fetch from RCSB)
3. Follow the 4-step preparation pipeline:
   • Step 1: Pocket Detection — define the binding site
   • Step 2: Grid Compilation — compute the scoring grid
   • Step 3: Validation — verify grid quality
   • Step 4: Review — confirm and save

See the Target Prep guide for detailed instructions on each step.

Step 4: Score Ligands

With a prepared target, you're ready to score:

Using IsoScore (Rescoring)

Best for: Large libraries, pre-docked poses, rapid screening.

1. Go to Workbench > IsoScore
2. Select your target
3. Upload your SDF file with pre-docked poses
4. Click Run — results appear in real-time at ~4,000 ligands/sec

Using IsoDock (Docking)

Best for: De novo pose prediction, smaller sets, when you need 3D poses.

1. Go to Workbench > IsoDock
2. Select your target
3. Upload your ligand SDF/MOL2 file
4. Click Run — each ligand takes ~3 seconds

See IsoDock and IsoScore guides for detailed usage.

Step 5: Analyze Results

After scoring completes:

1. Sort by score — lower (more negative) scores indicate stronger predicted binding
2. View 3D poses — click any ligand to see its docked pose in the 3D viewer
3. Inspect score decomposition — see how each physics term contributes to the total score
4. Export results — download CSV for further analysis in your preferred tools

Quick Reference

Next Steps

• Try the Demo — Run validated DEKOIS2 benchmarks to see LatticeZero in action
• Scoring Profiles — Learn how to customize scoring weights for your target class
• Golden Packs — Use pre-validated target bundles with known performance
• FAQ — Common questions and troubleshooting tips