InsilicoΣ
Drug Discovery, Cheminformatics & Bioinformatics
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New Molecule Generation

Generate 3D drug molecules inside a protein binding pocket

DecompDiff is not installed. Jobs can be created but will fail until the package is installed.
Upload target protein structure (PDB format, max 50 MB)
Pocket center will be computed from the ligand's center of mass
5-30 angstroms (default 10)
10-1000 molecules to generate
Cancel
How It Works
  1. Upload protein structure (PDB)
  2. Define the binding pocket (coordinates or reference ligand)
  3. DecompDiff decomposes molecules into arms + scaffold and generates 3D structures via diffusion
  4. Browse generated molecules with drug-likeness scores (QED, SA, MW, LogP)
Tips
  • Remove water molecules and heteroatoms from PDB
  • Use co-crystallized ligand for accurate pocket center
  • Pocket radius of 10A works well for most targets
  • Generate 100+ samples for diversity
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