We are pleased to announce the release of openfe version 1.12!

This release is anchored by a usability drive across the whole OpenFE ecosystem, alongside automated structural analysis for SepTop and a net charge transformation update to the Hybrid Topology Protocol for membrane-bound proteins.

Please see below for some highlights and see the Changelog for more details.

Ecosystem Usability Drive

This release pairs openfe with the latest versions of cinnabar, konnektor, kartograf, LOMAP, and openfe-analysis, each shipped as part of a wider push to improve usability and documentation across the ecosystem:

  • cinnabar (v0.6.0): a documentation rewrite with extensive tutorials, new plots and analyses drawn from our industry benchmarking paper, and support for pIC50 values in absolute predictions and plots.
  • konnektor (v0.4.0): a full documentation overhaul, critical bug fixes, and stronger test coverage.
  • kartograf (v2.0): updated defaults informed by our industry benchmark, plus an overhaul of documentation, structure, API, and guides.
  • LOMAP (v3.3.0): dropped the gufe dependency and deprecated broken components and its CLI.
  • openfe-analysis (v0.5.0): a refactor for usability and upcoming SepTop compatibility, alongside fixes for multi-chain and periodic-boundary handling and symmetry-corrected RMSD.

Automated Structural Analysis in SepTop

The SepTop protocol now performs automated structural analysis.

Protocol Updates

Net Charge Transformations for Membrane-Bound Proteins

The Hybrid Topology Protocol now supports net charge transformations for membrane-bound protein systems.

Element Change Warning Removed

We’ve removed the long-standing warning raised by the Hybrid Topology Protocol for mappings with element changes in core atoms. Element transformations using mass-averaged particles are now the default and have been thoroughly tested.

Unbiased Uncertainty Estimates

All Protocols now report the unbiased estimate of the standard deviation from the sample population — using Bessel’s correction (dividing by N-1 instead of N) — rather than the previous biased estimate. As a result, reported uncertainties are expected to be larger than before.

Changes and Deprecations

  • The Perses atom mapper (PersesAtomMapper and default_perses_scorer) has been removed.
  • LigandNetwork.to_rbfe_alchemical_network() is deprecated, and will be removed in openfe v1.13. This method was a redundant and confusing API entry point.

Installing openfe v1.12

openfe is made available as a conda-forge package, or docker and singularity images.

Please see our installation instructions for details on how to install openfe.