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choderalab / perses

Experiments with expanded ensembles to explore chemical space
http://perses.readthedocs.io
MIT License
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Update README? #1244

Open zhang-ivy opened 7 months ago

zhang-ivy commented 7 months ago

There is a notice in the README which states that Perses is pre-alpha, which is no longer true

The description also states "Experiments with expanded ensemble simulation to explore chemical and mutational space." -- which was the original intention but is also no longer accurate.

In addition to updating the README to address these two points, it may also be worth mentioning that Perses code will eventually be ported to OpenMMTools, feflow, openfe, etc

zhang-ivy commented 7 months ago

It would also be good to include the Zenodo software citation, and dominic's and my papers as ways to cite Perses.

Perses 0.10.1 citation (may need to generate new citations for the more recent releases): https://zenodo.org/records/6757402

Dominic's preprint: https://www.biorxiv.org/content/10.1101/2020.07.29.227959v1

My paper: https://pubs.acs.org/doi/full/10.1021/acs.jctc.3c00333