chore: update to version 1.1.0 with bug fix documentation

Author: amorehead

CHANGELOG.md

@@ -1,3 +1,12 @@
+### 1.1.0 - 03/20/2025
+
+**Changes**:
+
+- Fixed ligand scoring bug affecting the Astex Diverse, DockGen-E, and PoseBusters Benchmark datasets' primary-ligand results. Thanks a ton, @95028!
+- Regenerated results after addressing the scoring bug. The `notebooks` directory has been updated in the process.
+- Updated Zenodo links (for `forks` and `notebooks`).
+- An updated arXiv manuscript (v7) should be online soon.
+
 ### 1.0.0 - 11/04/2025
 
 **Changes**:

README.md

@@ -3,7 +3,7 @@
 # PoseBench
 
 [![Paper](http://img.shields.io/badge/arXiv-2405.14108-B31B1B.svg)](https://rdcu.be/eW5oj)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17536252.svg)](https://doi.org/10.5281/zenodo.17536252)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.19138652.svg)](https://doi.org/10.5281/zenodo.19138652)
 [![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/)
@@ -22,6 +22,8 @@ Comprehensive benchmarking of protein-ligand structure prediction methods
 
 [Documentation](https://bioinfomachinelearning.github.io/PoseBench/)
 
+> **⚠️ Notice:** We have discovered a bug in version `1.0.0` affecting the ligand scoring results of each primary-ligand dataset (Astex Diverse, DockGen-E, and PoseBusters Benchmark). We have addressed this bug in version `1.1.0`, which reports (~15% on average) reduced performance for each method currently in the benchmark. Please rerun your analyses if you have developed code on top of `PoseBench`. Thank you for your understanding!
+
 ## Contents
 
 - [Installation](#installation)
@@ -209,10 +211,10 @@ 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/17536252/files/astex_diverse_set.tar.gz
-wget https://zenodo.org/records/17536252/files/posebusters_benchmark_set.tar.gz
-wget https://zenodo.org/records/17536252/files/dockgen_set.tar.gz
-wget https://zenodo.org/records/17536252/files/casp15_set.tar.gz
+wget https://zenodo.org/records/19138652/files/astex_diverse_set.tar.gz
+wget https://zenodo.org/records/19138652/files/posebusters_benchmark_set.tar.gz
+wget https://zenodo.org/records/19138652/files/dockgen_set.tar.gz
+wget https://zenodo.org/records/19138652/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
@@ -228,39 +230,39 @@ rm casp15_set.tar.gz
 ```bash
 # fetch, extract, and clean-up benchmark method predictions to reproduce paper results (~19 GB) #
 # AutoDock Vina predictions and results
-wget https://zenodo.org/records/17536252/files/vina_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/19138652/files/vina_benchmark_method_predictions.tar.gz
 tar -xzf vina_benchmark_method_predictions.tar.gz
 rm vina_benchmark_method_predictions.tar.gz
 # DiffDock predictions and results
-wget https://zenodo.org/records/17536252/files/diffdock_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/19138652/files/diffdock_benchmark_method_predictions.tar.gz
 tar -xzf diffdock_benchmark_method_predictions.tar.gz
 rm diffdock_benchmark_method_predictions.tar.gz
 # DynamicBind predictions and results
-wget https://zenodo.org/records/17536252/files/dynamicbind_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/19138652/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/17536252/files/neuralplexer_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/19138652/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/17536252/files/rfaa_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/19138652/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/17536252/files/chai_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/19138652/files/chai_benchmark_method_predictions.tar.gz
 tar -xzf chai_benchmark_method_predictions.tar.gz
 rm chai_benchmark_method_predictions.tar.gz
 # Boltz-1 predictions and results
-wget https://zenodo.org/records/17536252/files/boltz_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/19138652/files/boltz_benchmark_method_predictions.tar.gz
 tar -xzf boltz_benchmark_method_predictions.tar.gz
 rm boltz_benchmark_method_predictions.tar.gz
 # AlphaFold 3 predictions and results
-wget https://zenodo.org/records/17536252/files/af3_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/19138652/files/af3_benchmark_method_predictions.tar.gz
 tar -xzf af3_benchmark_method_predictions.tar.gz
 rm af3_benchmark_method_predictions.tar.gz
 # CASP15 predictions and results for all methods
-wget https://zenodo.org/records/17536252/files/casp15_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/19138652/files/casp15_benchmark_method_predictions.tar.gz
 tar -xzf casp15_benchmark_method_predictions.tar.gz
 rm casp15_benchmark_method_predictions.tar.gz
 ```
@@ -270,7 +272,7 @@ rm casp15_benchmark_method_predictions.tar.gz
 ```bash
 # fetch, extract, and clean-up benchmark method interactions to reproduce paper results (~12 GB) #
 # cached ProLIF interactions for notebook plots
-wget https://zenodo.org/records/17536252/files/posebench_notebooks.tar.gz
+wget https://zenodo.org/records/19138652/files/posebench_notebooks.tar.gz
 tar -xzf posebench_notebooks.tar.gz
 rm posebench_notebooks.tar.gz
 ```
@@ -357,7 +359,7 @@ python3 posebench/data/components/protein_apo_to_holo_alignment.py dataset=casp1
 conda deactivate
 ```
 
-**NOTE:** The preprocessed Astex Diverse, PoseBusters Benchmark, DockGen, and CASP15 data available via [Zenodo](https://doi.org/10.5281/zenodo.17536252) 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](https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md).
+**NOTE:** The preprocessed Astex Diverse, PoseBusters Benchmark, DockGen, and CASP15 data available via [Zenodo](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](https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md).
 
 </details>
 

docs/source/conf.py

@@ -9,7 +9,7 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 project = "PoseBench"
 author = "Alex Morehead"
-release = "1.0.0"
+release = "1.1.0"
 copyright = f"{datetime.datetime.now().year}, {author}"
 
 # -- General configuration ---------------------------------------------------

docs/source/data_preparation.rst

@@ -6,4 +6,4 @@ How to prepare `PoseBench` data
     :end-line: 359
 
 .. note::
-    The preprocessed Astex Diverse, PoseBusters Benchmark, DockGen, and CASP15 data (available via Zenodo at https://doi.org/10.5281/zenodo.17536252) 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.
+    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.

notebooks/astex_method_interaction_analysis_plotting.ipynb

@@ -104,7 +104,7 @@
     ")\n",
     "assert os.path.exists(\n",
     "    ad_set_dir\n",
-    "), \"Please download the Astex Diverse set from `https://zenodo.org/records/17536252` before proceeding.\"\n",
+    "), \"Please download the Astex Diverse set from `https://zenodo.org/records/19138652` before proceeding.\"\n",
     "\n",
     "# Mappings\n",
     "method_mapping = {\n",

notebooks/astex_method_interaction_analysis_plotting.py

@@ -69,7 +69,7 @@
 )
 assert os.path.exists(
     ad_set_dir
-), "Please download the Astex Diverse set from `https://zenodo.org/records/17536252` before proceeding."
+), "Please download the Astex Diverse set from `https://zenodo.org/records/19138652` before proceeding."
 
 # Mappings
 method_mapping = {

notebooks/astex_method_interaction_analysis_plotting_slurm.py

@@ -70,7 +70,7 @@
 )
 assert os.path.exists(
     ad_set_dir
-), "Please download the Astex Diverse set from `https://zenodo.org/records/17536252` before proceeding."
+), "Please download the Astex Diverse set from `https://zenodo.org/records/19138652` before proceeding."
 
 # Mappings
 method_mapping = {

notebooks/casp15_method_interaction_analysis_plotting.ipynb

@@ -101,7 +101,7 @@
     ")\n",
     "assert os.path.exists(\n",
     "    casp15_set_dir\n",
-    "), \"Please download the (public) CASP15 set from `https://zenodo.org/records/17536252` before proceeding.\"\n",
+    "), \"Please download the (public) CASP15 set from `https://zenodo.org/records/19138652` before proceeding.\"\n",
     "\n",
     "# Mappings\n",
     "method_mapping = {\n",

notebooks/casp15_method_interaction_analysis_plotting.py

@@ -66,7 +66,7 @@
 )
 assert os.path.exists(
     casp15_set_dir
-), "Please download the (public) CASP15 set from `https://zenodo.org/records/17536252` before proceeding."
+), "Please download the (public) CASP15 set from `https://zenodo.org/records/19138652` before proceeding."
 
 # Mappings
 method_mapping = {

notebooks/casp15_method_interaction_analysis_plotting_slurm.py

@@ -67,7 +67,7 @@
 )
 assert os.path.exists(
     casp15_set_dir
-), "Please download the (public) CASP15 set from `https://zenodo.org/records/17536252` before proceeding."
+), "Please download the (public) CASP15 set from `https://zenodo.org/records/19138652` before proceeding."
 
 # Mappings
 method_mapping = {