Molecular docking service for protein–ligand binding
Send a protein structure and your compounds. ReactorMD prepares both, docks the ligands into the binding site you define, ranks the poses and returns the interactions, figures and a methods report in one organised package.
Who this service is for
- Pharmacy, biotechnology and chemistry students who need docking for a thesis or project
- PhD researchers screening a small series of designed or isolated compounds
- Teams that want a reproducible docking protocol with documented settings
What to send us
- A protein structure (PDB ID or your own file), or a sequence if a model has to be built first
- Ligands as SMILES, SDF or MOL2 files
- The binding site: a co-crystallised ligand, key residues or coordinates
- Optionally a reference inhibitor to compare against
How the work is done
- Review the receptor and clean it: remove unneeded water and duplicate chains, add hydrogens and assign protonation states.
- Prepare each ligand in 3D with sensible protonation, tautomer and energy-minimised geometry.
- Define the grid around your binding site and validate the protocol by re-docking a known ligand when one is available.
- Dock all ligands and keep several poses per compound.
- Rank by score, then inspect hydrogen bonds, hydrophobic contacts and pi interactions for the best poses.
- Package results: ranked table, 2D and 3D interaction figures, input files and a methods description.
What you receive
- Ranked docking table with scores for every ligand
- Best-pose structure files you can open in PyMOL, Chimera or Discovery Studio
- 2D interaction diagrams and 3D binding-site images
- Methods text describing preparation and settings, ready to adapt for a paper
- ZIP with all inputs and outputs for reproducibility
Package tiers & turnaround
| Ligand Volume | Price (USD) | Estimated Turnaround | Deliverables |
|---|---|---|---|
| Up to 10 ligands | $0.99 | Up to 4 hours | Prepared inputs, docked poses, score table, interaction figures & methods report (ZIP) |
| Up to 25 ligands | $2.49 | Up to 4 hours | Prepared inputs, docked poses, score table, interaction figures & methods report (ZIP) |
| Up to 50 ligands | $4.49 | Up to 4 hours | Prepared inputs, docked poses, score table, interaction figures & methods report (ZIP) |
| Up to 100 ligands | $7.99 | Up to 4 hours | Prepared inputs, docked poses, score table, interaction figures & methods report (ZIP) |
| Up to 250 ligands | $14.99 | Up to 8 hours | Prepared inputs, docked poses, score table, interaction figures & methods report (ZIP) |
| Up to 500 ligands | $24.99 | Up to 8 hours | Prepared inputs, docked poses, score table, interaction figures & methods report (ZIP) |
| Custom volume | Custom quote | Scope review | Tailored protocol & deliverables agreed before payment |
What this method can and cannot tell you
Docking scores are relative estimates, not measured binding affinities. They are most useful for comparing related compounds on the same receptor and for generating hypotheses. Strong candidates should be tested by molecular dynamics, free-energy methods and laboratory experiments.
Frequently asked questions
How much does online molecular docking cost?
ReactorMD docking starts at $0.99 for 10 ligands. The price shown at checkout depends on the number of ligands and any extra preparation your files need.
What files do I need to send for molecular docking?
A protein structure (a PDB ID is enough) and your ligands as SMILES, SDF or MOL2. If you know the binding site, tell us the key residues or the co-crystallised ligand.
Can you dock if I only have a protein sequence?
Yes. A homology model can be built first, then used for docking. See the homology modelling service.
Can I use the docking results in my thesis or paper?
The report includes a methods description and all settings so the work can be described and reproduced. As with any computational study, results should be interpreted alongside experimental evidence.
Is docking enough to prove a compound works?
No. Docking predicts a plausible pose and relative ranking. Follow-up molecular dynamics, MM/PBSA estimates and experimental assays are needed before drawing conclusions.
Related services
Ligand preparation for docking and virtual screening: standardisation, protonation and tautomer states, 3D generation, energy minimisation and format conversion.
ServiceVirtual screeningStructure-based virtual screening of compound libraries: library preparation, high-throughput docking, filtering and a ranked, traceable hit list.
ServiceMolecular dynamics simulationGROMACS molecular dynamics simulation of protein–ligand complexes with equilibration, production run and full trajectory analysis (RMSD, RMSF, Rg, SASA, H-bonds, PCA, FEL).
ServiceMM/PBSA binding free energyMM/PBSA and MM/GBSA binding free-energy estimates from molecular dynamics trajectories, with frame selection, energy decomposition and uncertainty reported.
Learn more
Ready to start?
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.