Workflow

the TargetGen pipeline, end to end

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PDBPocketDiffusionMolecules

A 3D-aware pipelinefrom structure to drug candidates.

Step 1
Input
PDB fetch / upload
RCSBPDB parser
Step 2
Detection
Find binding cavities
P2Rank 2.5
Step 3
Selection
Pocket / ligand / atom
3D viewermanual
Step 4
Generation
100-step diffusion
PocketXMol
Step 5
Filter & rank
Drug-likeness rerank
RDKitconstraints

P2Rank

ML pocket detector

Scores every solvent-accessible surface point on the protein for how ligand-friendly it looks, then clusters high-scoring points into pockets.

PocketXMol

Cell 2026 · foundation model

3D diffusion model. Starts from noise inside the pocket and iteratively refines atom positions and types over 100 steps until valid molecules emerge — pocket geometry stays fixed.

Inside a generation run

100 steps
t = 100
pure noise
Random atom cloud in pocket
t = 66
rough shape
Atoms drift toward geometry
t = 33
chemistry emerges
Elements + bonds crystallize
t = 0
valid molecule
Sanitized → SMILES + SDF
Try it now
3POZ · EGFR kinase
Open landing