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fhh2626 authored Sep 21, 2024
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Expand Up @@ -37,12 +37,16 @@ Simply run BFEE2Gui.py in terminal or PowerShell. One may need to use the absolu
A step-by-step tutorial is provided [here](https://www.nature.com/articles/s41596-021-00676-1).<br>
A tutorial about new streamlined geometrical route is provided in the SI of [this paper](https://pubs.acs.org/doi/full/10.1021/acs.jcim.3c00487).<br>

## Test files
One can download the Supplement Data [here](https://www.nature.com/articles/s41596-021-00676-1#Sec47) for testing BFEE2.

## Citations
When possible, please consider mentioning [Fu et al. Nat. Protoc. 2022, doi:10.1038/s41596-021-00676-1](https://www.nature.com/articles/s41596-021-00676-1#citeas) when BFEE2 is used in your project.


Additional references:<br>
BFEE2: [Fu et al. J. Chem. Inf. Model. 2021, 61, 2116–2123](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.1c00269)<br>
BFEE2 for protein-protein binding free energy calculations [Fu et al. J. Chem. Inf. Model. 2023, 63, 2512–2519](https://pubs.acs.org/doi/full/10.1021/acs.jcim.3c00487)<br>
Alchemical and geometric routes [Gumbart et al. J. Chem. Theory Comput. 2013, 9, 794–802](https://pubs.acs.org/doi/abs/10.1021/ct3008099)<br>
WTM-eABF: [Fu et al. Acc. Chem. Res. 2019, 52, 3254–3264](https://pubs.acs.org/doi/abs/10.1021/acs.accounts.9b00473) and [Fu et al. J. Phys. Chem. Lett. 2018, 9, 4738–4745](https://pubs.acs.org/doi/abs/10.1021/acs.jpclett.8b01994)<br>
Collective variables: [Fu et al. J. Chem. Theory Comput. 2017, 13, 5173–5178](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00791)<br>
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