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update: adjust line references in documentation after adding separate NMI link
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‎README.md‎

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# PoseBench
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[![Paper](http://img.shields.io/badge/arXiv-2405.14108-B31B1B.svg)](https://rdcu.be/eW5oj)
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[![arXiv](http://img.shields.io/badge/arXiv-2405.14108-B31B1B.svg)](https://arxiv.org/abs/2405.14108)
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[![NMI](http://img.shields.io/badge/Nature_Machine_Intelligence-B37A1B.svg)](https://rdcu.be/eW5oj)
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[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.19138652.svg)](https://doi.org/10.5281/zenodo.19138652)
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[![PyPI version](https://badge.fury.io/py/posebench.svg)](https://badge.fury.io/py/posebench)
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[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)

‎docs/source/acknowledgements.rst‎

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‎docs/source/available_methods.rst‎

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.. note::
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Have a new method to add? Please let us know by creating a pull request. We would be happy to work with you to integrate new methodology into this benchmark!

‎docs/source/bonus.rst‎

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.. image:: ./_static/WorkBench.jpeg
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:alt: My brain after building PoseBench

‎docs/source/citing_this_work.rst‎

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‎docs/source/comparative_plots.rst‎

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‎docs/source/data_preparation.rst‎

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.. note::
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The preprocessed Astex Diverse, PoseBusters Benchmark, DockGen, and CASP15 data (available via Zenodo at https://doi.org/10.5281/zenodo.19138652) provide pre-holo-aligned protein structures predicted by AlphaFold 3 (and alternatively MIT-licensed ESMFold) for these respective datasets. Accordingly, users must ensure their usage of such predicted protein structures from AlphaFold 3 aligns with AlphaFold 3's Terms of Use at https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md.

‎docs/source/ensemble_inference.rst‎

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In addition to having `consensus` as an available value for `ensemble_ranking_method`, one can also set `ensemble_ranking_method=ff` to have the method ensemble's top-ranked predictions selected using the criterion of "minimum (molecular dynamics) force field energy" (albeit while incurring a very large runtime complexity).

‎docs/source/for_developers.rst‎

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‎docs/source/index.rst‎

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.. image:: ./_static/PoseBench.png
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:alt: Overview of PoseBench
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