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11 changes: 7 additions & 4 deletions README.md
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# QligFEPv2 Benchmarking Experiments

This repository contains the benchmarking experiments for **QligFEPv2**, an iteration on the development of the QligFEP software for relative binding free energy (RBFE) calculations. QligFEP is a Python-based tool that automates the setup, execution, and analysis of free energy perturbation (FEP) calculations using the [Q simulation package](https://github.com/qusers/Q6).
This repository contains the benchmarking experiments for **QligFEPv2**, an iteration on the development of the QligFEP software for relative binding free energy (RBFE) calculations. QligFEP is a Python-based tool that automates the setup, execution, and analysis of free energy perturbation (FEP) calculations using the Q molecular dynamics engine.

**Original QligFEP publication:** Jespers, W., Esguerra, M., Åqvist, J., Gutiérrez-de-Terán, H., QligFEP: an automated workflow for small molecule free energy calculations in Q. *J Cheminform* **11**, 26 (2019). https://doi.org/10.1186/s13321-019-0348-5
The current work is currently available as a _preprint_ on ChemRxiv:
> Alencar Araripe D, Díaz Holguín A, Poso A, van Westen GJP, Åqvist J, Gutiérrez-de-Terán H, et al. QligFEP-2: an automated workflow for small molecule free energy calculations in Q. ChemRxiv. 2025; [doi:10.26434/chemrxiv-2025-x3r3z](https://doi.org/10.26434/chemrxiv-2025-x3r3z)

> 📄 *Manuscript describing this work is coming soon.*
## Installation

To reproduce the benchmarking results, we recommend users to setup an enviroment following the instructions in the [QligFEPv2 repository](https://github.com/qusers/Q). Additional dependencies for analysis and visualization are listed below under [Interactive Dashboard](#interactive-dashboard).

## Overview

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- **IndustryBenchmarks2024**: Baumann H., Alibay I., Horton J., Ries B., Henry M., *et al.*, OpenFreeEnergy/IndustryBenchmarks2024: v1.0.0 (v1.0.0). Zenodo. (2025) https://doi.org/10.5281/zenodo.17245550

- **Manuscript for this work**: *Coming soon*
- **QligFEP v2 preprint**: Alencar Araripe D, Díaz Holguín A, Poso A, van Westen GJP, Åqvist J, Gutiérrez-de-Terán H, _et al._ QligFEP-2: an automated workflow for small molecule free energy calculations in Q. ChemRxiv. 2025; [doi:10.26434/chemrxiv-2025-x3r3z](https://doi.org/10.26434/chemrxiv-2025-x3r3z)

## License

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