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Vecura

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MolScrub — Vecura

MolScrub

Process large numbers of small molecules for docking with AutoDock. Generates 3D coordinates using RDKit ETKDGv3 and UFF minimization, enumerates tautomers (low-energy states), enumerates pH corrections, converts boats to chairs for 6-member rings, and assigns partial charges (optional). Exposes both a Python API (Scrub class) and CLI (scrub.py).

Job Name

Input Molecules*

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

Target pH

pKa Model*

Skip Acid/Base Enumeration

Skip Tautomer Enumeration

Skip Ring Conformer Fixes

Skip 3D Coordinate Generation

Force Field*

Number of Initial Conformers

Keep All Fragments

Max Force Field Iterations

ETKDG Random Seed

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