Update Zenodo links

amorehead · amorehead · commit aebb10e18c91 · 2025-02-03T11:59:00.000-06:00
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,13 +1,16 @@
 ### 0.6.0 - TBD
 
-- Added new baseline methods
+- Added new baseline methods (AlphaFold 3, NeuralPLexer3, Chai-1 with multiple sequence alignments (MSAs))
 - Added new binding site-focused implementation of `complex_alignment.py` based on PyMOL's `align` command, which in many cases yields 3x better docking evaluation scores for baseline methods
 - Added new script for analyzing baseline methods' protein conformational changes w.r.t. input (e.g., AlphaFold) protein structures and the corresponding reference (crystal) protein structures
+- Added the new centroid RMSD and PLIF-EMD/WM metrics
+- Added a failure mode analysis notebook
 - Introducing DockGen-E, a new version of the DockGen benchmark dataset featuring enhanced biomolecular context for docking and co-folding predictions - namely, now all DockGen complexes represent the first (biologically relevant) bioassembly of the corresponding PDB structure
 - For the single-ligand datasets (i.e., Astex Diverse, PoseBusters Benchmark, and DockGen), now providing each baseline method with primary *and cofactor* ligand SMILES strings for prediction, to enhance the biomolecular context of these methods' predicted structures - as a result, for these single-ligand datasets, now the predicted ligand *most similar* to the primary ligand (in terms of both Tanimoto and structural similarity) is selected for scoring
-- Updated Chai-1's inference code to commit `44375d5d4ea44c0b5b7204519e63f40b063e4a7c`
+- Updated Chai-1's inference code to commit `44375d5d4ea44c0b5b7204519e63f40b063e4a7c`, and ran it also with NeuralPLexer3's (paired) MSAs
 - Replaced all AlphaFold 3 server predictions of each dataset's protein structures with predictions from AlphaFold 3's local inference code
-- With all the above changed in place, simplified, re-ran, and re-analyzed all baseline methods for each benchmark dataset, and updated the baseline predictions hosted on Zenodo
+- Pocket-only benchmarking has been deprecated
+- With all the above changed in place, simplified, re-ran, and re-analyzed all baseline methods for each benchmark dataset, and updated the baseline predictions and datasets (now containing standardized MSAs) hosted on Zenodo
 
 ### 0.5.0 - 09/30/2024
 
diff --git a/README.md b/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.13858866.svg)](https://doi.org/10.5281/zenodo.13858866)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14629652.svg)](https://doi.org/10.5281/zenodo.14629652)
 [![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/)
@@ -171,10 +171,10 @@ 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/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
+wget https://zenodo.org/records/14629652/files/astex_diverse_set.tar.gz
+wget https://zenodo.org/records/14629652/files/posebusters_benchmark_set.tar.gz
+wget https://zenodo.org/records/14629652/files/dockgen_set.tar.gz
+wget https://zenodo.org/records/14629652/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
@@ -190,31 +190,31 @@ 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/13858866/files/vina_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/14629652/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/13858866/files/diffdock_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/14629652/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/13858866/files/dynamicbind_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/14629652/files/dynamicbind_benchmark_method_predictions.tar.gz
 tar -xzf dynamicbind_benchmark_method_predictions.tar.gz
 rm dynamicbind_benchmark_method_predictions.tar.gz
 # RoseTTAFold-All-Atom predictions and results
-wget https://zenodo.org/records/13858866/files/rfaa_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/14629652/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/13858866/files/chai_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/14629652/files/chai_benchmark_method_predictions.tar.gz
 tar -xzf chai_benchmark_method_predictions.tar.gz
 rm chai_benchmark_method_predictions.tar.gz
 # AlphaFold 3 predictions and results
-wget https://zenodo.org/records/13858866/files/af3_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/14629652/files/af3_benchmark_method_predictions.tar.gz
 tar -xzf af3_benchmark_method_predictions.tar.gz
 rm af3_benchmark_method_predictions.tar.gz
 # NeuralPLexer3 predictions and results
-wget https://zenodo.org/records/13858866/files/neuralplexer3_benchmark_method_predictions.tar.gz
+wget https://zenodo.org/records/14629652/files/neuralplexer3_benchmark_method_predictions.tar.gz
 tar -xzf neuralplexer3_benchmark_method_predictions.tar.gz
 rm neuralplexer3_benchmark_method_predictions.tar.gz
 ```
@@ -224,7 +224,7 @@ rm neuralplexer3_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/13858866/files/posebench_notebooks.tar.gz
+wget https://zenodo.org/records/14629652/files/posebench_notebooks.tar.gz
 tar -xzf posebench_notebooks.tar.gz
 rm posebench_notebooks.tar.gz
 ```
@@ -311,7 +311,7 @@ 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.13858866) 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.14629652) 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>
 
diff --git a/notebooks/astex_method_interaction_analysis_plotting.ipynb b/notebooks/astex_method_interaction_analysis_plotting.ipynb
@@ -103,7 +103,7 @@
     ")\n",
     "assert os.path.exists(\n",
     "    ad_set_dir\n",
-    "), \"Please download the Astex Diverse set from `https://zenodo.org/records/13858866` before proceeding.\"\n",
+    "), \"Please download the Astex Diverse set from `https://zenodo.org/records/14629652` before proceeding.\"\n",
     "\n",
     "# Mappings\n",
     "method_mapping = {\n",
diff --git a/notebooks/astex_method_interaction_analysis_plotting.py b/notebooks/astex_method_interaction_analysis_plotting.py
@@ -68,7 +68,7 @@
 )
 assert os.path.exists(
     ad_set_dir
-), "Please download the Astex Diverse set from `https://zenodo.org/records/13858866` before proceeding."
+), "Please download the Astex Diverse set from `https://zenodo.org/records/14629652` before proceeding."
 
 # Mappings
 method_mapping = {
diff --git a/notebooks/casp15_method_interaction_analysis_plotting.ipynb b/notebooks/casp15_method_interaction_analysis_plotting.ipynb
@@ -100,7 +100,7 @@
     ")\n",
     "assert os.path.exists(\n",
     "    casp15_set_dir\n",
-    "), \"Please download the (public) CASP15 set from `https://zenodo.org/records/13858866` before proceeding.\"\n",
+    "), \"Please download the (public) CASP15 set from `https://zenodo.org/records/14629652` before proceeding.\"\n",
     "\n",
     "# Mappings\n",
     "method_mapping = {\n",
diff --git a/notebooks/casp15_method_interaction_analysis_plotting.py b/notebooks/casp15_method_interaction_analysis_plotting.py
@@ -65,7 +65,7 @@
 )
 assert os.path.exists(
     casp15_set_dir
-), "Please download the (public) CASP15 set from `https://zenodo.org/records/13858866` before proceeding."
+), "Please download the (public) CASP15 set from `https://zenodo.org/records/14629652` before proceeding."
 
 # Mappings
 method_mapping = {
diff --git a/notebooks/dataset_interaction_analysis_plotting.ipynb b/notebooks/dataset_interaction_analysis_plotting.ipynb
@@ -76,16 +76,16 @@
     ")\n",
     "assert os.path.exists(\n",
     "    ad_set_dir\n",
-    "), \"Please download the Astex Diverse set from `https://zenodo.org/records/13858866` before proceeding.\"\n",
+    "), \"Please download the Astex Diverse set from `https://zenodo.org/records/14629652` before proceeding.\"\n",
     "assert os.path.exists(\n",
     "    pb_set_dir\n",
-    "), \"Please download the PoseBusters Benchmark set from `https://zenodo.org/records/13858866` before proceeding.\"\n",
+    "), \"Please download the PoseBusters Benchmark set from `https://zenodo.org/records/14629652` before proceeding.\"\n",
     "assert os.path.exists(\n",
     "    dg_set_dir\n",
-    "), \"Please download the DockGen set from `https://zenodo.org/records/13858866` before proceeding.\"\n",
+    "), \"Please download the DockGen set from `https://zenodo.org/records/14629652` before proceeding.\"\n",
     "assert os.path.exists(\n",
     "    casp15_set_dir\n",
-    "), \"Please download the (public) CASP15 set from `https://zenodo.org/records/13858866` before proceeding.\"\n",
+    "), \"Please download the (public) CASP15 set from `https://zenodo.org/records/14629652` before proceeding.\"\n",
     "\n",
     "CASP15_ANALYSIS_TARGETS_TO_SKIP = [\n",
     "    \"T1170\"\n",
diff --git a/notebooks/dataset_interaction_analysis_plotting.py b/notebooks/dataset_interaction_analysis_plotting.py
@@ -41,16 +41,16 @@
 )
 assert os.path.exists(
     ad_set_dir
-), "Please download the Astex Diverse set from `https://zenodo.org/records/13858866` before proceeding."
+), "Please download the Astex Diverse set from `https://zenodo.org/records/14629652` before proceeding."
 assert os.path.exists(
     pb_set_dir
-), "Please download the PoseBusters Benchmark set from `https://zenodo.org/records/13858866` before proceeding."
+), "Please download the PoseBusters Benchmark set from `https://zenodo.org/records/14629652` before proceeding."
 assert os.path.exists(
     dg_set_dir
-), "Please download the DockGen set from `https://zenodo.org/records/13858866` before proceeding."
+), "Please download the DockGen set from `https://zenodo.org/records/14629652` before proceeding."
 assert os.path.exists(
     casp15_set_dir
-), "Please download the (public) CASP15 set from `https://zenodo.org/records/13858866` before proceeding."
+), "Please download the (public) CASP15 set from `https://zenodo.org/records/14629652` before proceeding."
 
 CASP15_ANALYSIS_TARGETS_TO_SKIP = [
     "T1170"
diff --git a/notebooks/dockgen_method_interaction_analysis_plotting.ipynb b/notebooks/dockgen_method_interaction_analysis_plotting.ipynb
@@ -103,7 +103,7 @@
     ")\n",
     "assert os.path.exists(\n",
     "    dg_set_dir\n",
-    "), \"Please download the DockGen set from `https://zenodo.org/records/13858866` before proceeding.\"\n",
+    "), \"Please download the DockGen set from `https://zenodo.org/records/14629652` before proceeding.\"\n",
     "\n",
     "# Mappings\n",
     "method_mapping = {\n",
diff --git a/notebooks/dockgen_method_interaction_analysis_plotting.py b/notebooks/dockgen_method_interaction_analysis_plotting.py
@@ -68,7 +68,7 @@
 )
 assert os.path.exists(
     dg_set_dir
-), "Please download the DockGen set from `https://zenodo.org/records/13858866` before proceeding."
+), "Please download the DockGen set from `https://zenodo.org/records/14629652` before proceeding."
 
 # Mappings
 method_mapping = {
diff --git a/notebooks/posebusters_method_interaction_analysis_plotting.ipynb b/notebooks/posebusters_method_interaction_analysis_plotting.ipynb
@@ -104,7 +104,7 @@
     ")\n",
     "assert os.path.exists(\n",
     "    pb_set_dir\n",
-    "), \"Please download the PoseBusters Benchmark set from `https://zenodo.org/records/13858866` before proceeding.\"\n",
+    "), \"Please download the PoseBusters Benchmark set from `https://zenodo.org/records/14629652` before proceeding.\"\n",
     "\n",
     "# PoseBusters Benchmark deposition dates\n",
     "pb_deposition_dates_filepath = \"posebusters_benchmark_complex_pdb_deposition_dates.csv\"\n",
diff --git a/notebooks/posebusters_method_interaction_analysis_plotting.py b/notebooks/posebusters_method_interaction_analysis_plotting.py
@@ -69,7 +69,7 @@
 )
 assert os.path.exists(
     pb_set_dir
-), "Please download the PoseBusters Benchmark set from `https://zenodo.org/records/13858866` before proceeding."
+), "Please download the PoseBusters Benchmark set from `https://zenodo.org/records/14629652` before proceeding."
 
 # PoseBusters Benchmark deposition dates
 pb_deposition_dates_filepath = "posebusters_benchmark_complex_pdb_deposition_dates.csv"

Original file line number	Diff line number	Diff line change
`@@ -68,7 +68,7 @@`
`68`	`68`	`)`
`69`	`69`	`assert os.path.exists(`
`70`	`70`	`ad_set_dir`
`71`		-), "Please download the Astex Diverse set from `https://zenodo.org/records/13858866` before proceeding."
	`71`	+), "Please download the Astex Diverse set from `https://zenodo.org/records/14629652` before proceeding."
`72`	`72`
`73`	`73`	`# Mappings`
`74`	`74`	`method_mapping = {`
Original file line number	Diff line number	Diff line change
`@@ -65,7 +65,7 @@`
`65`	`65`	`)`
`66`	`66`	`assert os.path.exists(`
`67`	`67`	`casp15_set_dir`
`68`		-), "Please download the (public) CASP15 set from `https://zenodo.org/records/13858866` before proceeding."
	`68`	+), "Please download the (public) CASP15 set from `https://zenodo.org/records/14629652` before proceeding."
`69`	`69`
`70`	`70`	`# Mappings`
`71`	`71`	`method_mapping = {`