Overview
The De Novo Drug Design tool generates novel small molecules that fit a target protein’s binding pocket. It uses state-of-the-art generative models to create drug candidates for hit discovery.Workflow
Upload protein structure
Provide a PDB file by uploading, pasting, or using the example structure. The 3D structure is visualized in the viewer.
Define binding pocket
Either:
- AI detection — The AI automatically identifies the binding pocket
- Manual coordinates — Specify pocket center coordinates (x, y, z) and radius
Configure generation
Select a model and parameters:
- Model: Pocket2Mol, TargetDiff, DiffSBDD, or DecompDiff
- Count: Number of molecules to generate
- Temperature: Creativity parameter (higher = more diverse)
Alex’s screenshot note: Take a screenshot of the De Novo setup wizard showing the protein structure viewer with the binding pocket highlighted.
Results
Generated molecules are displayed in a sortable table:| Column | Description |
|---|---|
| 2D Depiction | Molecular structure drawing |
| SMILES | SMILES string |
| QED | Drug-likeness score (0-1) |
| SA | Synthetic accessibility (1-10, lower = easier) |
| Vina Score | Predicted binding affinity |
| MW | Molecular weight |
| LogP | Lipophilicity |
Molecule Detail
Click any molecule to see:- Enlarged 2D depiction
- All properties
- SMILES string (copyable)
- Edit & Re-score — Modify the SMILES and recalculate properties
- Fragment Growing — Extend the molecule from specific attachment points
Export
| Format | Description |
|---|---|
| SDF | Standard molecular data format |
| SMILES | Plain text SMILES strings |
Jobs History
View past generation jobs with:- Job ID and date
- Model used
- Number of molecules generated
- Status (running, complete, failed)
Guided Demo
Click Guided Demo for a step-by-step walkthrough using an example protein that demonstrates the full workflow.Alex’s screenshot note: Take a screenshot of the results table showing 5-6 generated molecules with their 2D depictions and property scores.