QuantumBind Relative Binding Free Energy (RBFE)

Summary

QuantumBind RBFE is Acellera's implementation for Relative Binding Free Energy (RBFE) calculations. This approach is based on the Alchemical Transfer Method (ATM) and incorporates Neural Network Potentials (NNP) within a hybrid NNP/MM framework. The data in this repository was used in the accompanying manuscript: QuantumBind-RBFE: Accurate Relative Binding Free Energy Calculations Using Neural Network Potentials.

Contents

• inputs/: Contains input files for binding free energy calculations.
• results/: Includes ΔΔG and ΔG values from the runs presented in our manuscript.
• tutorial/: Provides a Jupyter notebook offering a step-by-step tutorial on setting up and running a QuantumBind-RBFE calculation.
• scripts/: Contains the necessary scripts to execute the production phase using the provided input files.

Prerequisites

QuantumBind-RBFE can be run via Acellera-ATM and HTMD, Acellera's molecular modeling environment. Please make sure that you have both repositories installed and properly configured to execute the scripts and workflows.

References

• AceFF:
  If you wish to use the AceFF model, Acellera's own NNP can be found on Hugging Face: AceFF 1.0.
  AceFF 1.0 is available for non-profit use and demonstrations, allowing researchers to explore its potential in their projects.