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Update Zenodo links
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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://arxiv.org/abs/2405.14108)
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[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11477766.svg)](https://doi.org/10.5281/zenodo.11477766)
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[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13858866.svg)](https://doi.org/10.5281/zenodo.13858866)
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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)
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[![Docs](https://assets.readthedocs.org/static/projects/badges/passing-flat.svg)](https://bioinfomachinelearning.github.io/PoseBench/)
@@ -154,10 +154,10 @@ of how to extend `PoseBench`, as outlined below.
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```bash
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# fetch, extract, and clean-up preprocessed Astex Diverse, PoseBusters Benchmark, DockGen, and CASP15 data (~3 GB) #
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wget https://zenodo.org/records/11477766/files/astex_diverse_set.tar.gz
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wget https://zenodo.org/records/11477766/files/posebusters_benchmark_set.tar.gz
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wget https://zenodo.org/records/11477766/files/dockgen_set.tar.gz
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wget https://zenodo.org/records/11477766/files/casp15_set.tar.gz
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wget https://zenodo.org/records/13858866/files/astex_diverse_set.tar.gz
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wget https://zenodo.org/records/13858866/files/posebusters_benchmark_set.tar.gz
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wget https://zenodo.org/records/13858866/files/dockgen_set.tar.gz
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wget https://zenodo.org/records/13858866/files/casp15_set.tar.gz
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tar -xzf astex_diverse_set.tar.gz
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tar -xzf posebusters_benchmark_set.tar.gz
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tar -xzf dockgen_set.tar.gz
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```bash
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# fetch, extract, and clean-up benchmark method predictions to reproduce paper results (~19 GB) #
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# DiffDock predictions and results
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wget https://zenodo.org/records/11477766/files/diffdock_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/13858866/files/diffdock_benchmark_method_predictions.tar.gz
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tar -xzf diffdock_benchmark_method_predictions.tar.gz
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rm diffdock_benchmark_method_predictions.tar.gz
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# FABind predictions and results
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wget https://zenodo.org/records/11477766/files/fabind_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/13858866/files/fabind_benchmark_method_predictions.tar.gz
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tar -xzf fabind_benchmark_method_predictions.tar.gz
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rm fabind_benchmark_method_predictions.tar.gz
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# DynamicBind predictions and results
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wget https://zenodo.org/records/11477766/files/dynamicbind_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/13858866/files/dynamicbind_benchmark_method_predictions.tar.gz
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tar -xzf dynamicbind_benchmark_method_predictions.tar.gz
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rm dynamicbind_benchmark_method_predictions.tar.gz
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# NeuralPLexer predictions and results
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wget https://zenodo.org/records/11477766/files/neuralplexer_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/13858866/files/neuralplexer_benchmark_method_predictions.tar.gz
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tar -xzf neuralplexer_benchmark_method_predictions.tar.gz
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rm neuralplexer_benchmark_method_predictions.tar.gz
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# RoseTTAFold-All-Atom predictions and results
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wget https://zenodo.org/records/11477766/files/rfaa_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/13858866/files/rfaa_benchmark_method_predictions.tar.gz
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tar -xzf rfaa_benchmark_method_predictions.tar.gz
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rm rfaa_benchmark_method_predictions.tar.gz
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# Chai-1 predictions and results
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wget https://zenodo.org/records/11477766/files/chai_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/13858866/files/chai_benchmark_method_predictions.tar.gz
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tar -xzf chai_benchmark_method_predictions.tar.gz
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rm chai_benchmark_method_predictions.tar.gz
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# TULIP predictions and results
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wget https://zenodo.org/records/11477766/files/tulip_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/13858866/files/tulip_benchmark_method_predictions.tar.gz
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tar -xzf tulip_benchmark_method_predictions.tar.gz
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rm tulip_benchmark_method_predictions.tar.gz
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# AutoDock Vina predictions and results
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wget https://zenodo.org/records/11477766/files/vina_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/13858866/files/vina_benchmark_method_predictions.tar.gz
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tar -xzf vina_benchmark_method_predictions.tar.gz
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rm vina_benchmark_method_predictions.tar.gz
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# Astex Diverse, PoseBusters Benchmark (w/ pocket-only results), DockGen, and CASP15 consensus ensemble predictions and results
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wget https://zenodo.org/records/11477766/files/astex_diverse_ensemble_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/11477766/files/posebusters_benchmark_ensemble_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/11477766/files/dockgen_ensemble_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/11477766/files/casp15_ensemble_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/13858866/files/astex_diverse_ensemble_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/13858866/files/posebusters_benchmark_ensemble_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/13858866/files/dockgen_ensemble_benchmark_method_predictions.tar.gz
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wget https://zenodo.org/records/13858866/files/casp15_ensemble_benchmark_method_predictions.tar.gz
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tar -xzf astex_diverse_ensemble_benchmark_method_predictions.tar.gz
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tar -xzf posebusters_benchmark_ensemble_benchmark_method_predictions.tar.gz
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tar -xzf dockgen_ensemble_benchmark_method_predictions.tar.gz
@@ -285,7 +285,7 @@ python3 posebench/data/components/protein_apo_to_holo_alignment.py dataset=poseb
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python3 posebench/data/components/protein_apo_to_holo_alignment.py dataset=astex_diverse num_workers=1
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```
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**NOTE:** The preprocessed Astex Diverse, PoseBusters Benchmark, DockGen, and CASP15 data available via [Zenodo](https://doi.org/10.5281/zenodo.11477766) provide pre-holo-aligned protein structures predicted by AlphaFold 3 for these respective datasets. Accordingly, users must ensure their usage of such predicted protein structures aligns with the AlphaFold Server's [Terms of Service](https://alphafoldserver.com/terms).
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**NOTE:** The preprocessed Astex Diverse, PoseBusters Benchmark, DockGen, and CASP15 data available via [Zenodo](https://doi.org/10.5281/zenodo.13858866) provide pre-holo-aligned protein structures predicted by AlphaFold 3 for these respective datasets. Accordingly, users must ensure their usage of such predicted protein structures aligns with the AlphaFold Server's [Terms of Service](https://alphafoldserver.com/terms).
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</details>
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‎notebooks/casp15_method_interaction_analysis_plotting.ipynb‎

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")\n",
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"assert os.path.exists(\n",
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" casp15_set_dir\n",
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"), \"Please download the (public) CASP15 set from `https://zenodo.org/records/11477766` before proceeding.\"\n",
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"), \"Please download the (public) CASP15 set from `https://zenodo.org/records/13858866` before proceeding.\"\n",
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"\n",
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"# Mappings\n",
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"method_mapping = {\n",

‎notebooks/dataset_interaction_analysis_plotting.ipynb‎

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")\n",
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"assert os.path.exists(\n",
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" ad_set_dir\n",
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"), \"Please download the Astex Diverse set from `https://zenodo.org/records/11477766` before proceeding.\"\n",
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"), \"Please download the Astex Diverse set from `https://zenodo.org/records/13858866` before proceeding.\"\n",
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"assert os.path.exists(\n",
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" pb_set_dir\n",
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"), \"Please download the PoseBusters Benchmark set from `https://zenodo.org/records/11477766` before proceeding.\"\n",
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"), \"Please download the PoseBusters Benchmark set from `https://zenodo.org/records/13858866` before proceeding.\"\n",
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"assert os.path.exists(\n",
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" dg_set_dir\n",
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"), \"Please download the DockGen set from `https://zenodo.org/records/11477766` before proceeding.\"\n",
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"), \"Please download the DockGen set from `https://zenodo.org/records/13858866` before proceeding.\"\n",
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"assert os.path.exists(\n",
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" casp15_set_dir\n",
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"), \"Please download the (public) CASP15 set from `https://zenodo.org/records/11477766` before proceeding.\"\n",
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"), \"Please download the (public) CASP15 set from `https://zenodo.org/records/13858866` before proceeding.\"\n",
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"\n",
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"CASP15_ANALYSIS_TARGETS_TO_SKIP = [\n",
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" \"T1170\"\n",

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