DEV ENVIRONMENT — TEST PAYMENTS ONLY · agent-edited · not production

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VDDW

Varroa Drug Design Workbench · Computational drug discovery for Varroa destructor

Target Protein

Ligand (SMILES)

Properties

MW—

LogP—

TPSA—

HBD—

HBA—

RotB—

Rings—

Lipinski—

Docking Parameters

Box size (Å)

Exhaustiveness

Poses

3D Structure Viewer

No structure loaded

Docking Results

Run a docking job to see results here.

Known Varroacide Compound Library

Click any compound to load its SMILES into the docking panel.

Varroa destructor Drug Targets

Varroa destructor has 20,162 proteins in UniProt (all unreviewed/TrEMBL). Zero AlphaFold structures are available — all structures require prediction via ColabFold or Boltz. Listed below are the confirmed drug targets with UniProt accessions.

About VDDW

The Varroa Drug Design Workbench bridges the gap between AI-generated candidate molecules (SMILES strings) and predicted protein-ligand binding poses with affinity estimates. It integrates RDKit for molecular property calculation, 3Dmol.js for 3D structure visualization, and AutoDock Vina for molecular docking.

How it works

Select a target protein — choose from confirmed Varroa destructor drug targets
Enter a ligand SMILES — or pick from the known varroacide library
Calculate properties — RDKit computes MW, LogP, TPSA, Lipinski compliance
Visualize in 3D — 3Dmol.js renders the protein structure and ligand poses
Run docking — AutoDock Vina predicts binding affinity and pose

Limitations (Phase 1)

All Varroa destructor protein structures require computational prediction (no experimental structures available)
Docking is limited to 2 concurrent jobs on the MAH server (2 CPU cores, 1.9 GB RAM)
Batch screening (>50 ligands) should be offloaded to Modal cloud GPU
AlphaFold 2/3 and ESMFold weights are non-commercial — Boltz (MIT) is the commercial-safe alternative

Integration

PRISM → VDDW: PRISM identifies targets, VDDW docks against them
MAH-VLAB → VDDW: Scientist bot generates SMILES, VDDW tests them
MAH-ARENA: VDDW outputs visible on the ARENA multi-agent dashboard