Docking & Binding · Open Free Energy consortium
OpenFE / Lomap
Plans and executes alchemical free energy perturbation networks to calculate relative ligand binding affinities.
What OpenFE / Lomap is
OpenFE / Lomap is a computational workflow developed by the Open Free Energy consortium for conducting alchemical free energy perturbation (FEP) calculations. It is designed to provide high-precision relative binding free energy evaluations for small-molecule ligand series against macromolecular targets.
The tool couples perturbation network planning with rigorous alchemical simulation execution. Lomap automatically designs the perturbation network connecting structurally related compounds, while OpenFE executes the underlying free energy simulations to compute binding energy differences (ΔΔG) alongside statistical uncertainty estimates.
This workflow is particularly targeted at high-stakes drug discovery decisions where heuristic or machine-learning affinity estimates place candidate compounds within the margin of noise, requiring rigorous alchemical evaluation to distinguish lead molecules.
Key facts
- Version
- 1.0
- Domain
- Docking
- Tasks
- Free energy calculation, FEP
- Receptor input
- Protein structure (PDB format)
- Ligand input
- Ligand series (SMILES format, one per line)
- Output
- Table of ΔΔG values per edge with statistical error
- GPU memory
- 80 GB
What you can use it for
- Relative binding free energy determination
- Calculates experimental-grade relative binding free energies (ΔΔG) across a series of small-molecule ligands targeting a defined receptor.
- Perturbation network generation
- Plans optimal perturbation networks connecting candidate SMILES ligands using Lomap prior to simulation.
- Resolution of close affinity predictions
- Distinguishes between lead compounds when fast affinity predictions yield differences that fall within computational noise.
Run it here
No installation and no GPU of your own: fill in the inputs and it runs on our servers. Results stay in your browser unless you sign in.
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OpenFE / Lomap
Strengths and limits
Good at
- Automates the full workflow from perturbation network planning with Lomap through to alchemical calculation execution with OpenFE.
- Provides statistical error estimates alongside ΔΔG calculations for each edge in the perturbation network.
- Delivers high-precision alchemical calculations when lower-resolution affinity estimates are insufficiently discriminative.
Watch out for
- Requires significant computational resources, specifying 80 GB of GPU memory.
- Calculations are structured as relative differences (ΔΔG per network edge) across related ligands rather than direct single-ligand absolute affinities.
Inputs and outputs
You provide
Receptor (PDB)
Ligand series (SMILES, one per line)
You get back
ΔΔG per edge with statistical error.
Licence
Commercial use permitted · MIT
The MIT licence allows use in commercial research and products.
Questions
Can I use OpenFE / Lomap commercially?
Commercial use permitted. The MIT licence allows use in commercial research and products.
How do I run OpenFE / Lomap without installing anything?
Use the form under “Run it here” on this page: fill in the inputs and press Run model. It runs on our servers on 4–8× A100/H100, typically in 12h, and a run costs about 84,000 credits. Visitors without an account get 1,000 credits a month.
What inputs are required to run the workflow?
The workflow requires a protein receptor structure in PDB format and a series of small-molecule ligands supplied as SMILES strings, formatted one per line.
What are the roles of Lomap and OpenFE in this tool?
Lomap plans the perturbation network connecting the compounds, and OpenFE executes the subsequent alchemical free energy calculations.
What outputs does OpenFE / Lomap produce?
It generates a table detailing the computed relative free energy difference (ΔΔG) and associated statistical error for each edge in the planned network.
What hardware resources are necessary?
The setup requires an 80 GB GPU.
Written from OpenFE / Lomap's own documentation. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.