Consensus Docking Pipeline
What is this tool?
A 3-stage consensus molecular docking pipeline that predicts protein 3D structure from amino acid sequence using ESMFold, screens small-molecule ligands with AutoDock Vina, and re-scores the top hits with GNINA CNN deep learning for improved ranking accuracy.
Enter a protein amino acid sequence and a list of ligand SMILES to run the full consensus screening workflow.
Last updated: July 2026 · Reviewed by VigyanLLM Research Team
VigyanLLM's molecular docking consensus pipeline integrates ESMFold for protein structure prediction, AutoDock Vina for rapid pose generation, and GNINA with CNN scoring for binding affinity refinement — all running locally with no data egress.
| Component | Function |
|---|---|
| ESMFold | Protein structure prediction from amino acid sequence |
| AutoDock Vina | Rapid ligand-protein pose generation and scoring |
| GNINA (CNN) | Deep learning binding affinity refinement (ΔG/kcal/mol) |
| Consensus Scoring | Weighted average of Vina + GNINA + CNN scores |
Ready to Run a Docking Screen
Enter a protein sequence and at least one ligand SMILES above, then click Run Consensus Docking. The 3-stage pipeline will predict the protein structure and rank ligands by consensus score.
Benchmarked Against Industry Standards
The consensus pipeline combines ESMFold (MIT), AutoDock Vina (Apache 2.0), and GNINA for drug-discovery-grade virtual screening.
ESMFold pLDDT Validation
pLDDT scores correlate with CASP14/15 competition results. Mean confidence ≥ 70% is the recommended threshold for reliable docking.
Vina Cross-Validation
AutoDock Vina scoring reproduced within 1.5 kcal/mol RMSD on PDBbind core set. Exhaustiveness=4 balances speed and accuracy.
GNINA CNN Refinement
CNN re-scoring improves hit rates by 20-35% over Vina alone on the DUD-E benchmark. Default CNN model trained on PDBbind v2020.
One Plan for Primer Design + Docking
All subscription plans now include both primer design and molecular docking credits. No more separate plans.
- 5 primer designs
- 2 docking runs
- Up to 50 ligands/run
- Full 3D viewer access
- Standard queue
- 250 primer designs/mo
- 50 docking runs/mo
- Up to 50 ligands/run
- Full 3D viewer + downloads
- Standard queue priority
- 2,000 primer designs/mo
- 500 docking runs/mo
- Up to 200 ligands/run
- 5 researcher seats
- Priority queue + support
- 7,500 primer designs/mo
- 2,000 docking runs/mo
- Unlimited ligands/run
- Unlimited seats
- API access + SLA