Ligand fixer
Use this when a ligand file fails RDKit, Meeko, or AutoDock-style preparation and needs safe cleanup before docking.
Use this when a ligand file fails RDKit, Meeko, or AutoDock-style preparation and needs safe cleanup before docking.
Clean and filter DNA sequences by removing or replacing non-standard nucleotide characters. Supports multiple filter modes including standard 4 bases, IUPAC ambiguity codes, and custom character sets.
Split large FASTA files into smaller chunks. Divide by sequence count or create individual files for each sequence.
Clean and filter protein sequences by removing or replacing non-standard amino acid characters. Supports multiple filter modes including standard 20 amino acids, IUPAC codes, and custom character sets.
PDB2PQR prepares protein structures for electrostatics calculations by adding missing atoms, predicting protonation states using PROPKA, and assigning atomic charges and radii from standard force fields.
Convert InChI strings into SMILES with batch support and downloadable outputs.
Convert MOL2 ligand files into SMILES strings for registration, filtering, and downstream analysis.
Ligand fixer is meant for ligand files that already exist but fail during RDKit, Meeko, or docking preparation. If AutoDock Vina, DiffDock, or another RDKit-based workflow rejects an SDF, MOL, or MOL2 ligand, this tool applies safe cleanup steps and re-exports a repaired SDF.
It is not the general "start from SMILES" path. If you have a trusted SMILES string and want to generate a fresh structure file, use SMILES to SDF instead.
Ligand fixer is designed for common failure modes such as:
SDF uploads that need to be split into separate ligandsUpload one or more ligand structure files, or paste one ligand block into the text area. Supported structure formats are:
| Format | Extensions |
|---|---|
| SDF / MDL Molfile | .sdf, .sd, .mol |
| Tripos MOL2 | .mol2 |
You can upload up to 10 public inputs per job. Multi-record SDF files are automatically split into separate entries and processed one by one.
| Setting | Description |
|---|---|
Sanitize and normalize | Runs RDKit cleanup and sanitization, plus targeted safe chemistry repairs where supported. |
Keep largest fragment | Removes salts and counterions by keeping only the largest fragment. |
Add hydrogens | Adds explicit hydrogens before export. |
Generate 3D coordinates | Generates a 3D conformer when the ligand has no usable 3D coordinates. |
Run docking preflight | Reports whether the repaired ligand appears ready for RDKit-based docking preparation. |
Merge outputs into one SDF | Returns one combined fixed_batch.sdf instead of separate repaired files. |
The tool is intentionally conservative. It focuses on repairs that are high-confidence enough to automate without silently inventing chemistry.
Current repair and normalization behavior includes:
SDF input into separate entriesN+When a ligand still cannot be sanitized safely, the tool does not force a guess. That entry fails, and the JSON report explains which ligand failed and why.
By default, each successful ligand is returned as its own repaired file with _fixed added to the original name, for example:
Ligand (3).sdf -> Ligand (3)_fixed.sdfpose.mol2 -> pose_fixed.sdfIf Merge outputs into one SDF is enabled, the tool returns a single fixed_batch.sdf instead of individual repaired SDF files.
Every job also includes:
ligand_fixer_report.json with per-entry success, failure, warnings, and preflight statusCan't kekulize mol.