Ligand preparation for docking and virtual screening
Docking is only as good as the ligand files it receives. ReactorMD standardises your compounds, assigns realistic protonation and tautomer states, generates minimised 3D structures and converts them to the formats your software needs.
Who this service is for
- Students whose ligand files fail or give odd docking results
- Groups preparing a library for virtual screening
- Anyone converting between SMILES, SDF, MOL2, PDB and PDBQT
What to send us
- Compounds as SMILES, SDF, MOL2, PDB or a spreadsheet of names
- Target pH (default 7.4) and any special requirements
- Required output format
How the work is done
- Read and validate structures, flagging invalid valences and missing atoms.
- Standardise: neutralise or protonate, remove salts and counter-ions, handle stereochemistry.
- Enumerate sensible tautomer and protonation states at the target pH.
- Generate 3D conformers and minimise the energy.
- Convert to the required format and run a final structure check.
What you receive
- Clean ligand files in your requested format
- A table of properties and any structures that were changed or rejected
- A short preparation log you can cite in your methods
Ligand preparation packages
| Compound Count | Price (USD) | Estimated Turnaround |
|---|---|---|
| Up to 100 ligands | $1.00 | Up to 4 hours |
| Up to 500 ligands | $2.99 | Up to 4 hours |
| Up to 750 ligands | $3.75 | Up to 6 hours |
| Up to 1,500 ligands | $6.50 | Up to 6 hours |
| Up to 5,000 ligands | $12.00 | Up to 12 hours |
| Custom volume | Custom quote | Scope review |
What this method can and cannot tell you
Automated preparation cannot know your chemistry. Unusual metal complexes, reactive species and ambiguous stereochemistry are flagged for your review rather than silently changed.
Frequently asked questions
What formats can you prepare ligands in?
Input can be SMILES, SDF, MOL2 or PDB. Output can be SDF, MOL2, PDB or PDBQT for common docking programs.
Why does protonation state matter for docking?
Charge and hydrogen-bonding patterns change with protonation. A wrongly charged ligand can lose or gain interactions and distort scores.
Can you prepare a whole library?
Yes. For hundreds or thousands of compounds, contact ReactorMD for a quote.
Do you generate 3D structures from 2D drawings?
Yes. 3D coordinates are generated and energy-minimised as part of preparation.
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Tell us about your target and compounds. The price and scope are confirmed before payment.
Computational results are predictions and support, but do not replace, experimental validation. Page reviewed by ReactorMD, 16 October 2026.