Platform Workflow
A visual overview of the LatticeZero IsoPose scoring and validation pipeline — from target preparation through lead optimization and export.
Pipeline Stages
1. Upload PDB
Upload a receptor structure in PDB format, or choose from the pre-validated target library (46 GOLD_LOCKED targets available at launch).
2. Select Target
Choose the binding site and configure the receptor grid. For library targets, the binding site is pre-defined with validated pocket coordinates.
3. Configure Docking
Set docking parameters: exhaustiveness, scoring profile, and conformer options. FFT docking mode is available for PoseCompass-certified targets.
4. Run IsoPose (WebGPU)
IsoPose performs GPU-accelerated molecular docking directly in the browser using WebGPU compute shaders. Typical throughput: 50-200 ligands/second depending on hardware.
Fast Path — IsoScore: For pre-docked libraries, IsoScore provides ultra-fast rescoring at ~4,000 ligands/second without re-docking. This is useful for rapid virtual screening of large compound sets.
5. Optimize Scoring Profile
Use the Autotune optimizer to calibrate scoring weights for your target. Two modes are available:
- Unsupervised mode — classifies target family and generates weights automatically
- Labeled mode — uses known active/inactive labels to train a target-specific profile via logistic regression
Both docking results and IsoScore results feed back into the optimizer to improve discrimination.
6. Validate
Statistical validation ensures the scoring profile is robust:
- Cross-validation (CV) — k-fold AUC to measure generalization
- Y-scramble — permutation test to rule out overfitting
- Bootstrap — confidence intervals on AUC and enrichment metrics
7. Export Results
Download results in multiple formats:
- CSV — ranked ligand list with scores, poses, and ADME properties
- JSON — structured output for programmatic integration
- PDF — formatted report with plots and statistics
LP+ Lead Optimization (Optional)
For validated hits, the LP+ module provides FEP-calibrated binding affinity predictions to guide lead optimization. This step is optional and can be entered after any scoring or validation stage.
Alternate Entry Points
Not every project follows the full pipeline. Common abbreviated workflows:
| Workflow | Entry Point | Exits At |
|---|---|---|
| Quick screen | Upload PDB | Dock AUC + Poses |
| Rescore existing poses | IsoScore | Export Results |
| Profile calibration | Optimize Scoring Profile | Validate |
| Full discovery | Upload PDB | Export Results |