Update docs and citation

amorehead · amorehead · commit c266d132e53b · 2025-08-11T13:43:51.000-05:00
diff --git a/README.md b/README.md
@@ -1336,7 +1336,7 @@ If you use the code or benchmark method predictions associated with this reposit
 
 ```bibtex
 @inproceedings{morehead2024posebench,
-  title={Deep Learning for Protein-Ligand Docking: Are We There Yet?},
+  title={Assessing the potential of deep learning for protein-ligand docking},
   author={Morehead, Alex and Giri, Nabin and Liu, Jian and Neupane, Pawan and Cheng, Jianlin},
   booktitle={ICML AI4Science Workshop},
   year={2024},
diff --git a/citation.bib b/citation.bib
@@ -1,5 +1,5 @@
 @inproceedings{morehead2024posebench,
-  title={Deep Learning for Protein-Ligand Docking: Are We There Yet?},
+  title={Assessing the potential of deep learning for protein-ligand docking},
   author={Morehead, Alex and Giri, Nabin and Liu, Jian and Neupane, Pawan and Cheng, Jianlin},
   booktitle={ICML AI4Science Workshop},
   year={2024},
diff --git a/docs/source/_static/PoseBench.png b/docs/source/_static/PoseBench.png
diff --git a/docs/source/acknowledgements.rst b/docs/source/acknowledgements.rst
@@ -2,5 +2,5 @@ Acknowledgements
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 1178
-    :end-line: 1198
+    :start-line: 1309
+    :end-line: 1332
diff --git a/docs/source/available_methods.rst b/docs/source/available_methods.rst
@@ -2,8 +2,8 @@ Available inference methods
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 327
-    :end-line: 370
+    :start-line: 367
+    :end-line: 412
 
 .. note::
     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!
diff --git a/docs/source/bonus.rst b/docs/source/bonus.rst
@@ -2,8 +2,8 @@ Bonus
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 1216
-    :end-line: 1218
+    :start-line: 1350
+    :end-line: 1352
 
 .. image:: ./_static/WorkBench.jpeg
   :alt: My brain after building PoseBench
diff --git a/docs/source/citing_this_work.rst b/docs/source/citing_this_work.rst
@@ -2,5 +2,5 @@ Citing this work
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 1200
-    :end-line: 1212
+    :start-line: 1334
+    :end-line: 1346
diff --git a/docs/source/comparative_plots.rst b/docs/source/comparative_plots.rst
@@ -2,5 +2,5 @@ How to create comparative plots of inference results
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 1108
-    :end-line: 1134
+    :start-line: 1237
+    :end-line: 1265
diff --git a/docs/source/configs/data.rst b/docs/source/configs/data.rst
@@ -7,26 +7,49 @@ This section describes the configurations for various data-related scripts.
 Input data components
 ------------------------
 
-These data component configurations are used to modify how the input (apo) protein structures are predicted or aligned.
+These data component configurations are used to modify how the input (apo) protein structures are predicted, aligned, or analyzed or how one data format is converted to another.
 
-Protein apo-to-holo alignment
+Convert mmCIF to PDB
 ^^^^^^^^^^^^^^^^^^^^^^^^
-.. literalinclude:: ../../../configs/data/components/protein_apo_to_holo_alignment.yaml
+.. literalinclude:: ../../../configs/data/components/convert_mmcif_to_pdb.yaml
     :language: yaml
-    :caption: :file:`data/components/protein_apo_to_holo_alignment.yaml`
+    :caption: :file:`data/components/convert_mmcif_to_pdb.yaml`
+
+ESMFold sequence preparation
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/data/components/esmfold_sequence_preparation.yaml
+    :language: yaml
+    :caption: :file:`data/components/esmfold_sequence_preparation.yaml`
 
 FASTA preparation
 ^^^^^^^^^^^^^^^^^^^^^^^^
 .. literalinclude:: ../../../configs/data/components/fasta_preparation.yaml
     :language: yaml
     :caption: :file:`data/components/fasta_preparation.yaml`
 
-ESMFold sequence preparation
+Plot dataset RMSD
 ^^^^^^^^^^^^^^^^^^^^^^^^
-.. literalinclude:: ../../../configs/data/components/esmfold_sequence_preparation.yaml
+.. literalinclude:: ../../../configs/data/components/plot_dataset_rmsd.yaml
     :language: yaml
-    :caption: :file:`data/components/esmfold_sequence_preparation.yaml`
+    :caption: :file:`data/components/plot_dataset_rmsd.yaml`
 
+Prepare Boltz-1 MSAs
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/data/components/prepare_boltz_msas.yaml
+    :language: yaml
+    :caption: :file:`data/components/prepare_boltz_msas.yaml`
+
+Prepare Chai-1 MSAs
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/data/components/prepare_chai_msas.yaml
+    :language: yaml
+    :caption: :file:`data/components/prepare_chai_msas.yaml`
+
+Protein apo-to-holo alignment
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/data/components/protein_apo_to_holo_alignment.yaml
+    :language: yaml
+    :caption: :file:`data/components/protein_apo_to_holo_alignment.yaml`
 
 Method data parsers
 ------------------------
@@ -93,6 +116,18 @@ Chai-1 output extraction
     :language: yaml
     :caption: :file:`data/chai_output_extraction.yaml`
 
+Boltz-1 input preparation
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/data/boltz_input_preparation.yaml
+    :language: yaml
+    :caption: :file:`data/boltz_input_preparation.yaml`
+
+Boltz-1 output extraction
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/data/boltz_output_extraction.yaml
+    :language: yaml
+    :caption: :file:`data/boltz_output_extraction.yaml`
+
 AlphaFold 3 output extraction
 ^^^^^^^^^^^^^^^^^^^^^^^^
 .. literalinclude:: ../../../configs/data/af3_output_extraction.yaml
diff --git a/docs/source/configs/model.rst b/docs/source/configs/model.rst
@@ -51,6 +51,12 @@ Chai-1 inference
     :language: yaml
     :caption: :file:`model/chai_inference.yaml`
 
+Boltz-1 inference
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/model/boltz_inference.yaml
+    :language: yaml
+    :caption: :file:`model/boltz_inference.yaml`
+
 Vina inference
 ^^^^^^^^^^^^^^^^^^^^^^^^
 .. literalinclude:: ../../../configs/model/vina_inference.yaml
diff --git a/docs/source/data_preparation.rst b/docs/source/data_preparation.rst
@@ -2,8 +2,8 @@ How to prepare `PoseBench` data
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 171
-    :end-line: 319
+    :start-line: 207
+    :end-line: 359
 
 .. note::
     The preprocessed Astex Diverse, PoseBusters Benchmark, DockGen, and CASP15 data (available via Zenodo at https://doi.org/10.5281/zenodo.16791095) 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.
diff --git a/docs/source/ensemble_inference.rst b/docs/source/ensemble_inference.rst
@@ -2,8 +2,8 @@ How to run inference with a method ensemble
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 1049
-    :end-line: 1100
+    :start-line: 1178
+    :end-line: 1229
 
 .. note::
     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).
diff --git a/docs/source/for_developers.rst b/docs/source/for_developers.rst
@@ -2,5 +2,5 @@ For developers
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 1140
-    :end-line: 1174
+    :start-line: 1271
+    :end-line: 1305
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -9,16 +9,16 @@ Welcome to PoseBench's documentation!
 
 .. mdinclude:: ../../README.md
     :start-line: 4
-    :end-line: 13
+    :end-line: 14
 
 .. image:: ./_static/PoseBench.png
   :alt: Overview of PoseBench
   :align: center
   :width: 600
 
 .. mdinclude:: ../../README.md
-    :start-line: 19
-    :end-line: 21
+    :start-line: 20
+    :end-line: 22
 
 
 .. toctree::
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -2,5 +2,5 @@ Installation
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 42
-    :end-line: 153
+    :start-line: 43
+    :end-line: 189
diff --git a/docs/source/method_inference.rst b/docs/source/method_inference.rst
@@ -2,5 +2,5 @@ How to run inference with individual methods
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 398
-    :end-line: 1043
+    :start-line: 440
+    :end-line: 1172
diff --git a/docs/source/sweep_inference.rst b/docs/source/sweep_inference.rst
@@ -2,8 +2,8 @@ How to run a sweep of benchmarking experiments
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 378
-    :end-line: 390
+    :start-line: 420
+    :end-line: 434
 
 .. note::
     See the config file `configs/scripts/build_inference_script.yaml` for more details.
diff --git a/docs/source/tutorials.rst b/docs/source/tutorials.rst
@@ -2,5 +2,5 @@ Tutorials
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 159
-    :end-line: 165
+    :start-line: 195
+    :end-line: 201
