Update Zenodo links

README.md

@@ -3,7 +3,7 @@
 # PoseBench
 
 [![Paper](http://img.shields.io/badge/arXiv-2405.14108-B31B1B.svg)](https://arxiv.org/abs/2405.14108)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11477766.svg)](https://doi.org/10.5281/zenodo.11477766)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13858866.svg)](https://doi.org/10.5281/zenodo.13858866)
 [![PyPI version](https://badge.fury.io/py/posebench.svg)](https://badge.fury.io/py/posebench)
 [![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](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.
 
 ```bash
 # fetch, extract, and clean-up preprocessed Astex Diverse, PoseBusters Benchmark, DockGen, and CASP15 data (~3 GB) #
-wget https://zenodo.org/records/11477766/files/astex_diverse_set.tar.gz
-wget https://zenodo.org/records/11477766/files/posebusters_benchmark_set.tar.gz
-wget https://zenodo.org/records/11477766/files/dockgen_set.tar.gz
-wget https://zenodo.org/records/11477766/files/casp15_set.tar.gz
+wget https://zenodo.org/records/13858866/files/astex_diverse_set.tar.gz
+wget https://zenodo.org/records/13858866/files/posebusters_benchmark_set.tar.gz
+wget https://zenodo.org/records/13858866/files/dockgen_set.tar.gz
+wget https://zenodo.org/records/13858866/files/casp15_set.tar.gz
 tar -xzf astex_diverse_set.tar.gz
 tar -xzf posebusters_benchmark_set.tar.gz
 tar -xzf dockgen_set.tar.gz
@@ -173,42 +173,42 @@ rm casp15_set.tar.gz
 ```bash
 # fetch, extract, and clean-up benchmark method predictions to reproduce paper results (~19 GB) #
 # DiffDock predictions and results
-wget https://zenodo.org/records/11477766/files/diffdock_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/13858866/files/diffdock_benchmark_method_predictions.tar.gz
 tar -xzf diffdock_benchmark_method_predictions.tar.gz
 rm diffdock_benchmark_method_predictions.tar.gz
 # FABind predictions and results
-wget https://zenodo.org/records/11477766/files/fabind_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/13858866/files/fabind_benchmark_method_predictions.tar.gz
 tar -xzf fabind_benchmark_method_predictions.tar.gz
 rm fabind_benchmark_method_predictions.tar.gz
 # DynamicBind predictions and results
-wget https://zenodo.org/records/11477766/files/dynamicbind_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/13858866/files/dynamicbind_benchmark_method_predictions.tar.gz
 tar -xzf dynamicbind_benchmark_method_predictions.tar.gz
 rm dynamicbind_benchmark_method_predictions.tar.gz
 # NeuralPLexer predictions and results
-wget https://zenodo.org/records/11477766/files/neuralplexer_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/13858866/files/neuralplexer_benchmark_method_predictions.tar.gz
 tar -xzf neuralplexer_benchmark_method_predictions.tar.gz
 rm neuralplexer_benchmark_method_predictions.tar.gz
 # RoseTTAFold-All-Atom predictions and results
-wget https://zenodo.org/records/11477766/files/rfaa_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/13858866/files/rfaa_benchmark_method_predictions.tar.gz
 tar -xzf rfaa_benchmark_method_predictions.tar.gz
 rm rfaa_benchmark_method_predictions.tar.gz
 # Chai-1 predictions and results
-wget https://zenodo.org/records/11477766/files/chai_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/13858866/files/chai_benchmark_method_predictions.tar.gz
 tar -xzf chai_benchmark_method_predictions.tar.gz
 rm chai_benchmark_method_predictions.tar.gz
 # TULIP predictions and results
-wget https://zenodo.org/records/11477766/files/tulip_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/13858866/files/tulip_benchmark_method_predictions.tar.gz
 tar -xzf tulip_benchmark_method_predictions.tar.gz
 rm tulip_benchmark_method_predictions.tar.gz
 # AutoDock Vina predictions and results
-wget https://zenodo.org/records/11477766/files/vina_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/13858866/files/vina_benchmark_method_predictions.tar.gz
 tar -xzf vina_benchmark_method_predictions.tar.gz
 rm vina_benchmark_method_predictions.tar.gz
 # Astex Diverse, PoseBusters Benchmark (w/ pocket-only results), DockGen, and CASP15 consensus ensemble predictions and results
-wget https://zenodo.org/records/11477766/files/astex_diverse_ensemble_benchmark_method_predictions.tar.gz
-wget https://zenodo.org/records/11477766/files/posebusters_benchmark_ensemble_benchmark_method_predictions.tar.gz
-wget https://zenodo.org/records/11477766/files/dockgen_ensemble_benchmark_method_predictions.tar.gz
-wget https://zenodo.org/records/11477766/files/casp15_ensemble_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/13858866/files/astex_diverse_ensemble_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/13858866/files/posebusters_benchmark_ensemble_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/13858866/files/dockgen_ensemble_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/13858866/files/casp15_ensemble_benchmark_method_predictions.tar.gz
 tar -xzf astex_diverse_ensemble_benchmark_method_predictions.tar.gz
 tar -xzf posebusters_benchmark_ensemble_benchmark_method_predictions.tar.gz
 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
 python3 posebench/data/components/protein_apo_to_holo_alignment.py dataset=astex_diverse num_workers=1
 ```
 
-**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).
+**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).
 
 </details>
 

notebooks/casp15_method_interaction_analysis_plotting.ipynb

@@ -94,7 +94,7 @@
     ")\n",
     "assert os.path.exists(\n",
     "    casp15_set_dir\n",
-    "), \"Please download the (public) CASP15 set from `https://zenodo.org/records/11477766` before proceeding.\"\n",
+    "), \"Please download the (public) CASP15 set from `https://zenodo.org/records/13858866` before proceeding.\"\n",
     "\n",
     "# Mappings\n",
     "method_mapping = {\n",

notebooks/dataset_interaction_analysis_plotting.ipynb

@@ -78,16 +78,16 @@
     ")\n",
     "assert os.path.exists(\n",
     "    ad_set_dir\n",
-    "), \"Please download the Astex Diverse set from `https://zenodo.org/records/11477766` before proceeding.\"\n",
+    "), \"Please download the Astex Diverse set from `https://zenodo.org/records/13858866` before proceeding.\"\n",
     "assert os.path.exists(\n",
     "    pb_set_dir\n",
-    "), \"Please download the PoseBusters Benchmark set from `https://zenodo.org/records/11477766` before proceeding.\"\n",
+    "), \"Please download the PoseBusters Benchmark set from `https://zenodo.org/records/13858866` before proceeding.\"\n",
     "assert os.path.exists(\n",
     "    dg_set_dir\n",
-    "), \"Please download the DockGen set from `https://zenodo.org/records/11477766` before proceeding.\"\n",
+    "), \"Please download the DockGen set from `https://zenodo.org/records/13858866` before proceeding.\"\n",
     "assert os.path.exists(\n",
     "    casp15_set_dir\n",
-    "), \"Please download the (public) CASP15 set from `https://zenodo.org/records/11477766` before proceeding.\"\n",
+    "), \"Please download the (public) CASP15 set from `https://zenodo.org/records/13858866` before proceeding.\"\n",
     "\n",
     "CASP15_ANALYSIS_TARGETS_TO_SKIP = [\n",
     "    \"T1170\"\n",