Ligand fixer repairs and normalizes small molecule files for use in RDKit-based docking and cheminformatics workflows. It handles the common pre-processing steps — sanitization, salt stripping, hydrogen addition, and 3D embedding — that raw ligand files from databases or collaborators often need before they can be used reliably in tools like AutoDock Vina or Meeko.
Mixed-format batches are supported: a single job can include SDF, MOL, MOL2, and SMILES inputs simultaneously. Multi-record SDF files are split automatically into individual entries.
Ligand fixer is available directly in the browser with no software to install.
Paste a SMILES string, MOL block, MOL2 block, or SDF record into the text area — or upload files in any supported format. Mixed uploads (e.g., one SDF file and one SMILES file) are handled in a single job. Multi-record SDF files are automatically split into per-entry outputs.
| Format | Extensions |
|---|---|
| SDF / MDL Molfile | .sdf, .sd, .mol |
| Tripos MOL2 | .mol2 |
| SMILES | .smi, .smiles, .txt, .csv, .tsv |
| PubChem fetch | Compound name or CID |
Up to 10 entries (or 10 files) per job.
| Setting | Description |
|---|---|
Sanitize and normalize | Runs RDKit sanitization and safe normalization steps to correct common chemistry representation issues (default: on). |
Keep largest fragment | Strips salts, counterions, and solvate molecules by retaining only the largest fragment (default: on). |
Add hydrogens | Adds explicit hydrogens before export (default: on). Most docking tools require explicit hydrogens for proper atom typing. |
Generate 3D coordinates | Embeds a 3D conformer when the input lacks usable 3D coordinates (default: on). |
Run docking preflight | Reports whether each repaired ligand passes basic readiness checks for RDKit-based docking preparation (default: on). |
Each successfully repaired ligand is exported as an individual .sdf file. A combined batch.sdf is also produced. When Run docking preflight is enabled, the output includes a per-entry preflight summary indicating any remaining issues.
Most ligand quality issues fall into a few recurring categories:
Keep largest fragment option removes these.Generate 3D coordinates embeds a conformer using RDKit's distance geometry implementation.Add hydrogens makes them explicit, as required by Meeko, AutoDock, and related tools.