From 06eaf8893bea854c55f48d39dec7c268e782e6f9 Mon Sep 17 00:00:00 2001
From: Terence Lim <terencelim@ne47.bio>
Date: Thu, 13 Aug 2026 09:38:44 +0800
Subject: [PATCH 1/2] add opendde docs and missing protenixv2

---
 source/python-api/api-reference/fold.rst | 17 ++++++++++++++++-
 source/rest-api/fold.rst                 |  1 +
 2 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/source/python-api/api-reference/fold.rst b/source/python-api/api-reference/fold.rst
index 2908c474..495f6c3d 100644
--- a/source/python-api/api-reference/fold.rst
+++ b/source/python-api/api-reference/fold.rst
@@ -13,12 +13,21 @@ Interface
    :undoc-members:
 
 
-Models 
+Models
 ------
 
+.. autoclass:: openprotein.fold.OpenDDEModel
+   :members:
+
+.. autoclass:: openprotein.fold.OpenDDEAbagModel
+   :members:
+
 .. autoclass:: openprotein.fold.ProtenixModel
    :members:
 
+.. autoclass:: openprotein.fold.ProtenixV2Model
+   :members:
+
 .. autoclass:: openprotein.fold.Boltz2Model
    :members:
 
@@ -49,6 +58,12 @@ Models
 Results
 -------
 
+.. autoclass:: openprotein.fold.OpenDDEConfidence
+   :members:
+
+.. autoclass:: openprotein.fold.ProtenixConfidence
+   :members:
+
 .. autoclass:: openprotein.fold.ESMFold2Confidence
    :members:
 
diff --git a/source/rest-api/fold.rst b/source/rest-api/fold.rst
index bf55ddc4..797e7497 100644
--- a/source/rest-api/fold.rst
+++ b/source/rest-api/fold.rst
@@ -11,6 +11,7 @@ Currently, we support the following models:
 - **AlphaFold2**: Open-sourced Alphafold 2 implementation using ColabFold. `GitHub link <https://github.com/sokrypton/ColabFold>`__, `Reference <https://www.nature.com/articles/s41592-022-01488-1>`__. Licensed under `MIT <https://choosealicense.com/licenses/mit/>`__.
 - **Boltz-2, Boltz-1x, Boltz-1**: Open-source Boltz models. `GitHub link <https://github.com/jwohlwend/boltz>`__, `Boltz-1 reference <https://www.biorxiv.org/content/10.1101/2024.11.19.624167v1>`__, `Boltz-2 <https://www.biorxiv.org/content/10.1101/2025.06.14.659707v1>`__. Licensed under `MIT <https://choosealicense.com/licenses/mit/>`__. 
 - **Protenix**: Open-source Protenix model. `GitHub link <https://github.com/bytedance/Protenix>`_, `Reference <https://www.biorxiv.org/content/early/2026/02/22/2026.02.05.703733.1>`_. Licensed under `Apache-2.0 <https://choosealicense.com/licenses/apache-2.0/>`_.
+- **OpenDDE, OpenDDE-abag**: Open-source OpenDDE all-atom co-folding models, predicting protein, DNA, RNA, ligand and ion complexes in a single structure. ``opendde-abag`` is tuned on antibody-antigen complexes. `GitHub link <https://github.com/aurekaresearch/OpenDDE>`__, `Reference <https://arxiv.org/abs/2607.03787>`__. Licensed under `Apache-2.0 <https://choosealicense.com/licenses/apache-2.0/>`__.
 - **RosettaFold-3**: Open-source RosettaFold-3 model. `GitHub link <https://github.com/RosettaCommons/modelforge>`__, `Reference <https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2>`__. Licensed under `BSD-3 <https://choosealicense.com/licenses/bsd-3-clause/>`__. 
 
 Endpoints

From 31a4efa4c5a3099fef405dbe3fbd4327357aa826 Mon Sep 17 00:00:00 2001
From: Mark Gee <markgee@ne47.bio>
Date: Thu, 20 Aug 2026 15:12:00 -0400
Subject: [PATCH 2/2] docs: move protenix-v2 entries to #199

---
 source/python-api/api-reference/fold.rst | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/source/python-api/api-reference/fold.rst b/source/python-api/api-reference/fold.rst
index 495f6c3d..3eeaecce 100644
--- a/source/python-api/api-reference/fold.rst
+++ b/source/python-api/api-reference/fold.rst
@@ -25,9 +25,6 @@ Models
 .. autoclass:: openprotein.fold.ProtenixModel
    :members:
 
-.. autoclass:: openprotein.fold.ProtenixV2Model
-   :members:
-
 .. autoclass:: openprotein.fold.Boltz2Model
    :members:
 
@@ -61,9 +58,6 @@ Results
 .. autoclass:: openprotein.fold.OpenDDEConfidence
    :members:
 
-.. autoclass:: openprotein.fold.ProtenixConfidence
-   :members:
-
 .. autoclass:: openprotein.fold.ESMFold2Confidence
    :members: