Structural readiness
Track the exact protein structure, construct, cofactors, ligand pose, and preparation context required by the calculation.
RBFE and ABFE workflows
Use free energy calculations where the structural series supports them.
Qualify the protein-ligand system, map ligand transformations, submit configured free energy calculations, and review estimates with uncertainty, convergence context, and the artifacts needed to challenge the result.
FEPRBFEABFELigand mappingUncertaintyCycle closure
Prerequisites before compute
Make system qualification part of the FEP result.
MolexIO ties each run to an exact target structure, selected pocket or complex, ligand identities, mapping, method, engine configuration, and artifacts. A missing prepared pose or unsuitable transformation is a readiness problem—not a reason to invent a free energy estimate.
Series qualification
Review common scaffold, charge changes, stereochemistry, binding-mode assumptions, and transformation complexity before network design.
RBFE networks
Organize pairwise transformations across a congeneric series and retain the graph used to infer relative affinity differences.
ABFE context
Use absolute calculations only with the additional restraints, sampling, and interpretation appropriate to the configured method.
Quality signals
Inspect uncertainty, overlap, convergence, cycle closure, failures, and missing edges before interpreting small numerical differences.
Traceable artifacts
Keep inputs, mapped systems, logs, trajectories or summaries, engine versions, and normalized outputs attached to the project run.
A defensible FEP workflow
Qualify, simulate, diagnose, then compare.
- 01
Qualify the system
Confirm exact structure, binding pose, protonation, cofactors, waters, and series suitability.
- 02
Build the network
Map chemically reasonable transformations and document topology or charge risks.
- 03
Run and monitor
Execute the configured engine while preserving parameters, progress, failures, and artifacts.
- 04
Review uncertainty
Interpret estimates only after convergence, consistency, and experimental context are considered.
Scientific boundary
Precision in the output does not guarantee accuracy in the model.
Free energy estimates depend on the force field, sampling, protonation and tautomer states, binding mode, water network, protein state, ligand mapping, and convergence. Differences smaller than the relevant uncertainty should not be treated as decisive. Prospective experimental comparison remains essential for assessing the method in each chemical series.
Questions before use
FEP FAQ
When is RBFE appropriate?
Usually for a congeneric series with a credible shared binding mode and transformations the selected method can represent reliably.
Does a result equal experimental affinity?
No. It is a model-based estimate with structural, force-field, sampling, and convergence limitations.
Why review uncertainty and cycle closure?
They help expose unstable or inconsistent calculations before rank differences are used.
Connect FEP estimates to the exact system that produced them.
Keep structural prerequisites, mapping, quality diagnostics, and experimental context visible during series decisions.