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SigmaDock — Vecura

SigmaDock

Fragment-based SE(3) diffusion model for protein-ligand molecular docking (re-docking and cross-docking). Predicts ligand pose given protein pocket PDB + ligand SDF; supports optional reference ligand SDF for cross-docking pocket/CoM. Optional GNINA Vina/Vinardo rescoring and PoseBusters validation.

Job Name

Protein PDB*

Ligands (SMILES)*

Plain list (no header)

CC(=O)Oc1ccccc1
COc1ccc(cc1)C(=O)N

CSV with header (smiles required, name optional)

smiles,name
CC(=O)Oc1ccccc1,Aspirin

Pocket Center

X

Y

Z

Reference Ligand SDF

Num Seeds

seeds

Num Diffusion Steps

steps

Pocket Distance Cutoff

Å

Noise Scale

Noise Decay

Solver*

Discretization*

Fragmentation Strategy*

Scoring*

PoseBusters Config*

Random Seed

Configure input settings on the left, then click "Run"