Choosing the Right Tool

LatticeZero has three main scoring tools: QuickDock, IsoPose, and IsoScore. Here's when to use each.

Quick Comparison

QuickDock

Use when: You have a compound idea and want a fast answer.

QuickDock is optimized for speed and simplicity. Paste a SMILES, pick a target, click Dock. Ideal for:

• Quickly triaging a list of compound ideas
• First-pass evaluation before investing in synthesis
• Sharing a result with collaborators via link
• Testing whether a scaffold is worth exploring

Limitations: One pose per compound, limited customization, no SDF upload.

→ QuickDock Guide · Launch QuickDock

IsoPose

Use when: You need full control over the docking process or detailed binding mode analysis.

IsoPose is the full docking engine with complete parameter control. Use it for:

• Lead optimization - docking a series of analogs with consistent settings
• Binding mode analysis - multiple poses, interaction diagrams, 3D viewer
• Preparing data for SAR analysis
• High-confidence docking for compounds near synthesis

Key features:

• Batch docking (multiple ligands at once)
• Conformer ensemble mode (better poses for flexible molecules)
• Custom scoring profiles
• PoseRepair-Lite (clash resolution)
• Water anchor mode (conserved water networks)

→ IsoPose Guide · Launch IsoPose

IsoScore

Use when: You already have a docked pose and want physics analysis.

IsoScore takes an existing 3D pose and runs the full 14-term physics decomposition. Use it for:

• Analyzing why a specific compound scores well or poorly
• Comparing the same pose under different scoring profiles
• Rescoring poses docked by an external program (AutoDock, Glide, etc.)
• Understanding which interactions to optimize in an analog

Key features:

• 4 scoring tiers (Lite / Standard / Elite / CLI-Parity)
• Full physics breakdown per term
• Profile comparison mode
• Ultra-fast (~4,000 ligands/second for batch rescoring)

→ IsoScore Guide · Launch IsoScore

The Typical Workflow

For serious lead discovery, the tools chain together naturally:

Compound idea
     ↓
QuickDock     ← "Is this worth investigating?" (seconds)
     ↓ (hits)
IsoPose       ← "How does it bind? What pose looks right?" (minutes)
     ↓ (top poses)
IsoScore      ← "Why does it score this way? What should I optimize?" (seconds)
     ↓
Design Dashboard / SAR Explorer  ← Multi-parameter optimization

Target Prep

Before docking against a custom target (not in the validated library), you need to prepare the receptor. Target Prep guides you through a 4-step workflow:

1. Upload - PDB file or RCSB code
2. Diagnose - identify issues (waters, metals, missing atoms)
3. Adjust - configure pocket center, radius, waters, metal coordination
4. Validate - verify the prepared target by re-docking a reference compound

Target Prep only needs to run once per target; the prepared target can be reused across all docking sessions.

Autotune

For custom targets where you don't have benchmark data (actives/decoys), Autotune generates a scoring profile by interpolating from 27 pre-validated profiles. It requires only the receptor PDB and a set of candidate ligands - no labels needed.