Automate relative binding free energy calculations with OpenFE.
npx skills add https://github.com/Genentech/openfe_skill --skill openfe
Please help me install this Agent Skill. Skill: OpenFE Source: https://github.com/Genentech/openfe_skill/tree/main Command: npx skills add https://github.com/Genentech/openfe_skill --skill openfe
This Skill automates the process of predicting relative binding free energy using OpenFE, a powerful Python package for alchemical free energy calculations.
Use the OpenFE skill to plan and run the RBFE calculation for a given protein and ligand pair with the Hybrid protocol:
go to /path/to/protein_and_ligand, use OpenFE hybrid
High-intent search queries and answers about installing and using this skill.
Relative binding free energy calculations are automated by this Skill using OpenFE to predict protein-ligand interactions. It applies to various biological systems and supports planning and executing the RBFE calculation network.
Alchemical free energy calculation predicts binding affinities between proteins and ligands. You need it in drug discovery research to estimate relative binding free energies and identify promising compounds.
Yes, performing complex alchemical free energy calculations requires OpenMM and RDKit. You also need OpenFE, kartograf, openff-units, and click to automate the RBFE process.
The best way to plan an RBFE calculation network is using OpenFE, which automates network planning and execution. You can use Hybrid or SepTop protocols for different binding energy calculation types.
Yes, the OpenFE Skill supports both SepTop and Hybrid protocols for binding free energy calculations. You can select either protocol when planning your RBFE calculation network.
To start an OpenFE hybrid RBFE calculation, specify the path to your protein and ligand files. The Skill automates the relative binding free energy calculation process end-to-end.
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