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-  sha256: 6e82527920600883088c5825f5d4a5bd06a2676d4958d4f3bc622bad2439c0ac
+  version: 1.19.1
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   - jupyter-fs[fs]>=1.0 ; extra == 'dev'
   - jupyter-server!=2.11 ; extra == 'dev'
-  - marimo>=0.17.6 ; extra == 'dev'
+  - marimo>=0.17.6,<=0.19.4 ; extra == 'dev'
   - nbconvert ; extra == 'dev'
   - pre-commit ; extra == 'dev'
   - pytest ; extra == 'dev'
@@ -1587,7 +1587,7 @@ packages:
   - isort ; extra == 'test-external'
   - jupyter-fs[fs]>=1.0 ; extra == 'test-external'
   - jupyter-server!=2.11 ; extra == 'test-external'
-  - marimo>=0.17.6 ; extra == 'test-external'
+  - marimo>=0.17.6,<=0.19.4 ; extra == 'test-external'
   - nbconvert ; extra == 'test-external'
   - pre-commit ; extra == 'test-external'
   - pytest ; extra == 'test-external'
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+  version: 3.10.1
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   - mkdocs>=1.6 ; extra == 'docs'
   - mkdocs-nature>=0.6 ; extra == 'docs'
   - mdx-gh-links>=0.2 ; extra == 'docs'
-  - mkdocstrings[python] ; extra == 'docs'
+  - mkdocstrings[python]>=0.28.3 ; extra == 'docs'
   - mkdocs-gen-files ; extra == 'docs'
   - mkdocs-section-index ; extra == 'docs'
   - mkdocs-literate-nav ; extra == 'docs'
@@ -2003,10 +2003,10 @@ packages:
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+- pypi: https://files.pythonhosted.org/packages/0d/4b/8d5f796a792f8a25f6925a96032f098789f448571eb92011df1ae59e8ea8/nbconvert-7.17.0-py3-none-any.whl
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-  version: 7.16.6
-  sha256: 1375a7b67e0c2883678c48e506dc320febb57685e5ee67faa51b18a90f3a712b
+  version: 7.17.0
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   requires_dist:
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   - bleach[css]!=5.0.0
@@ -2024,6 +2024,7 @@ packages:
   - pygments>=2.4.1
   - traitlets>=5.1
   - flaky ; extra == 'all'
+  - intersphinx-registry ; extra == 'all'
   - ipykernel ; extra == 'all'
   - ipython ; extra == 'all'
   - ipywidgets>=7.5 ; extra == 'all'
@@ -2033,15 +2034,16 @@ packages:
   - pydata-sphinx-theme ; extra == 'all'
   - pyqtwebengine>=5.15 ; extra == 'all'
   - pytest>=7 ; extra == 'all'
-  - sphinx==5.0.2 ; extra == 'all'
+  - sphinx>=5.0.2 ; extra == 'all'
   - sphinxcontrib-spelling ; extra == 'all'
   - tornado>=6.1 ; extra == 'all'
+  - intersphinx-registry ; extra == 'docs'
   - ipykernel ; extra == 'docs'
   - ipython ; extra == 'docs'
   - myst-parser ; extra == 'docs'
   - nbsphinx>=0.2.12 ; extra == 'docs'
   - pydata-sphinx-theme ; extra == 'docs'
-  - sphinx==5.0.2 ; extra == 'docs'
+  - sphinx>=5.0.2 ; extra == 'docs'
   - sphinxcontrib-spelling ; extra == 'docs'
   - pyqtwebengine>=5.15 ; extra == 'qtpdf'
   - pyqtwebengine>=5.15 ; extra == 'qtpng'
@@ -2051,7 +2053,7 @@ packages:
   - ipywidgets>=7.5 ; extra == 'test'
   - pytest>=7 ; extra == 'test'
   - playwright ; extra == 'webpdf'
-  requires_python: '>=3.8'
+  requires_python: '>=3.9'
 - pypi: https://files.pythonhosted.org/packages/a9/82/0340caa499416c78e5d8f5f05947ae4bc3cba53c9f038ab6e9ed964e22f1/nbformat-5.10.4-py3-none-any.whl
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+- pypi: https://files.pythonhosted.org/packages/25/7a/1fee4329abc705a469a4afe6e69b1ef7e915117747886327104a8493a955/numpy-2.4.2-cp314-cp314-macosx_11_0_arm64.whl
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-  version: 2.4.1
-  sha256: e867df947d427cdd7a60e3e271729090b0f0df80f5f10ab7dd436f40811699c3
+  version: 2.4.2
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-- pypi: https://files.pythonhosted.org/packages/eb/c0/3ed5083d94e7ffd7c404e54619c088e11f2e1939a9544f5397f4adb1b8ba/numpy-2.4.1-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
+- pypi: https://files.pythonhosted.org/packages/5d/6c/7f237821c9642fb2a04d2f1e88b4295677144ca93285fd76eff3bcba858d/numpy-2.4.2-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
   name: numpy
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-  sha256: 2f44de05659b67d20499cbc96d49f2650769afcb398b79b324bb6e297bfe3844
+  version: 2.4.2
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-- pypi: https://files.pythonhosted.org/packages/8f/c6/70f9bde77022d0017a91b4b405554f1b142b15f822639e9d4b6d3530313d/openprotein_python-0.10.0-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/59/fb/22dedf3ac872ef193d4c88cf645c9125f819c1367b276cdcf4a8a5202d14/openprotein_python-0.11.1-py3-none-any.whl
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+  version: 0.11.1
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@@ -2129,7 +2131,7 @@ packages:
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   - tomli>=2.3.0,<3
   - tqdm>=4.66.5,<5
-  requires_python: '>=3.10,<3.13'
+  requires_python: '>=3.10,<3.15'
 - conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.0-h26f9b46_0.conda
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   md5: 9ee58d5c534af06558933af3c845a780
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+- pypi: https://files.pythonhosted.org/packages/b7/b9/c538f279a4e237a006a2c98387d081e9eb060d203d8ed34467cc0f0b9b53/packaging-26.0-py3-none-any.whl
   name: packaging
-  version: '25.0'
-  sha256: 29572ef2b1f17581046b3a2227d5c611fb25ec70ca1ba8554b24b0e69331a484
+  version: '26.0'
+  sha256: b36f1fef9334a5588b4166f8bcd26a14e521f2b55e6b9de3aaa80d3ff7a37529
   requires_python: '>=3.8'
 - pypi: https://files.pythonhosted.org/packages/15/b2/0e62f78c0c5ba7e3d2c5945a82456f4fac76c480940f805e0b97fcbc2f65/pandas-2.3.3-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
   name: pandas
@@ -2356,10 +2358,10 @@ packages:
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   - types-setuptools==67.2.0.1 ; extra == 'qa'
   requires_python: '>=3.6'
-- pypi: https://files.pythonhosted.org/packages/32/2b/121e912bd60eebd623f873fd090de0e84f322972ab25a7f9044c056804ed/pathspec-1.0.3-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/ef/3c/2c197d226f9ea224a9ab8d197933f9da0ae0aac5b6e0f884e2b8d9c8e9f7/pathspec-1.0.4-py3-none-any.whl
   name: pathspec
-  version: 1.0.3
-  sha256: e80767021c1cc524aa3fb14bedda9c34406591343cc42797b386ce7b9354fb6c
+  version: 1.0.4
+  sha256: fb6ae2fd4e7c921a165808a552060e722767cfa526f99ca5156ed2ce45a5c723
   requires_dist:
   - hyperscan>=0.7 ; extra == 'hyperscan'
   - typing-extensions>=4 ; extra == 'optional'
@@ -2476,10 +2478,10 @@ packages:
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   requires_python: '>=3.8'
-- pypi: https://files.pythonhosted.org/packages/29/f8/40e01c350ad9a2b3cb4e6adbcc8a83b17ee50dd5792102b6142385937db5/psutil-7.2.1-cp36-abi3-manylinux2010_x86_64.manylinux_2_12_x86_64.manylinux_2_28_x86_64.whl
+- pypi: https://files.pythonhosted.org/packages/80/c4/f5af4c1ca8c1eeb2e92ccca14ce8effdeec651d5ab6053c589b074eda6e1/psutil-7.2.2-cp36-abi3-macosx_11_0_arm64.whl
   name: psutil
-  version: 7.2.1
-  sha256: 5e38404ca2bb30ed7267a46c02f06ff842e92da3bb8c5bfdadbd35a5722314d8
+  version: 7.2.2
+  sha256: 1a7b04c10f32cc88ab39cbf606e117fd74721c831c98a27dc04578deb0c16979
   requires_dist:
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   - pytest ; extra == 'dev'
@@ -2506,16 +2508,24 @@ packages:
   - virtualenv ; extra == 'dev'
   - vulture ; extra == 'dev'
   - wheel ; extra == 'dev'
+  - colorama ; os_name == 'nt' and extra == 'dev'
+  - pyreadline3 ; os_name == 'nt' and extra == 'dev'
+  - pywin32 ; implementation_name != 'pypy' and os_name == 'nt' and extra == 'dev'
+  - wheel ; implementation_name != 'pypy' and os_name == 'nt' and extra == 'dev'
+  - wmi ; implementation_name != 'pypy' and os_name == 'nt' and extra == 'dev'
   - psleak ; extra == 'test'
   - pytest ; extra == 'test'
   - pytest-instafail ; extra == 'test'
   - pytest-xdist ; extra == 'test'
   - setuptools ; extra == 'test'
+  - pywin32 ; implementation_name != 'pypy' and os_name == 'nt' and extra == 'test'
+  - wheel ; implementation_name != 'pypy' and os_name == 'nt' and extra == 'test'
+  - wmi ; implementation_name != 'pypy' and os_name == 'nt' and extra == 'test'
   requires_python: '>=3.6'
-- pypi: https://files.pythonhosted.org/packages/c5/2c/78e4a789306a92ade5000da4f5de3255202c534acdadc3aac7b5458fadef/psutil-7.2.1-cp36-abi3-macosx_11_0_arm64.whl
+- pypi: https://files.pythonhosted.org/packages/b5/70/5d8df3b09e25bce090399cf48e452d25c935ab72dad19406c77f4e828045/psutil-7.2.2-cp36-abi3-manylinux2010_x86_64.manylinux_2_12_x86_64.manylinux_2_28_x86_64.whl
   name: psutil
-  version: 7.2.1
-  sha256: 05cc68dbb8c174828624062e73078e7e35406f4ca2d0866c272c2410d8ef06d1
+  version: 7.2.2
+  sha256: 076a2d2f923fd4821644f5ba89f059523da90dc9014e85f8e45a5774ca5bc6f9
   requires_dist:
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@@ -2542,11 +2552,19 @@ packages:
   - virtualenv ; extra == 'dev'
   - vulture ; extra == 'dev'
   - wheel ; extra == 'dev'
+  - colorama ; os_name == 'nt' and extra == 'dev'
+  - pyreadline3 ; os_name == 'nt' and extra == 'dev'
+  - pywin32 ; implementation_name != 'pypy' and os_name == 'nt' and extra == 'dev'
+  - wheel ; implementation_name != 'pypy' and os_name == 'nt' and extra == 'dev'
+  - wmi ; implementation_name != 'pypy' and os_name == 'nt' and extra == 'dev'
   - psleak ; extra == 'test'
   - pytest ; extra == 'test'
   - pytest-instafail ; extra == 'test'
   - pytest-xdist ; extra == 'test'
   - setuptools ; extra == 'test'
+  - pywin32 ; implementation_name != 'pypy' and os_name == 'nt' and extra == 'test'
+  - wheel ; implementation_name != 'pypy' and os_name == 'nt' and extra == 'test'
+  - wmi ; implementation_name != 'pypy' and os_name == 'nt' and extra == 'test'
   requires_python: '>=3.6'
 - pypi: https://files.pythonhosted.org/packages/22/a6/858897256d0deac81a172289110f31629fc4cee19b6f01283303e18c8db3/ptyprocess-0.7.0-py2.py3-none-any.whl
   name: ptyprocess
@@ -2963,10 +2981,10 @@ packages:
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   - statsmodels>=0.12 ; extra == 'stats'
   requires_python: '>=3.8'
-- pypi: https://files.pythonhosted.org/packages/e0/76/f963c61683a39084aa575f98089253e1e852a4417cb8a3a8a422923a5246/setuptools-80.10.1-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/94/b8/f1f62a5e3c0ad2ff1d189590bfa4c46b4f3b6e49cef6f26c6ee4e575394d/setuptools-80.10.2-py3-none-any.whl
   name: setuptools
-  version: 80.10.1
-  sha256: fc30c51cbcb8199a219c12cc9c281b5925a4978d212f84229c909636d9f6984e
+  version: 80.10.2
+  sha256: 95b30ddfb717250edb492926c92b5221f7ef3fbcc2b07579bcd4a27da21d0173
   requires_dist:
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@@ -2982,7 +3000,6 @@ packages:
   - tomli-w>=1.0.0 ; extra == 'test'
   - pytest-timeout ; extra == 'test'
   - pytest-perf ; sys_platform != 'cygwin' and extra == 'test'
-  - pyobjc<12 ; python_full_version < '3.10' and sys_platform == 'darwin' and extra == 'test'
   - jaraco-develop>=7.21 ; python_full_version >= '3.9' and sys_platform != 'cygwin' and extra == 'test'
   - pytest-home>=0.5 ; extra == 'test'
   - pytest-subprocess ; extra == 'test'
@@ -3404,12 +3421,13 @@ packages:
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   sha256: d6241c1a16b1c9e4cc28148b1cda97dd1c6cb4fb7068ac1bedc610768dff0ba9
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+- pypi: https://files.pythonhosted.org/packages/16/e1/3079a9ff9b8e11b846c6ac5c8b5bfb7ff225eee721825310c91b3b50304f/tqdm-4.67.3-py3-none-any.whl
   name: tqdm
-  version: 4.67.1
-  sha256: 26445eca388f82e72884e0d580d5464cd801a3ea01e63e5601bdff9ba6a48de2
+  version: 4.67.3
+  sha256: ee1e4c0e59148062281c49d80b25b67771a127c85fc9676d3be5f243206826bf
   requires_dist:
   - colorama ; sys_platform == 'win32'
+  - importlib-metadata ; python_full_version < '3.8'
   - pytest>=6 ; extra == 'dev'
   - pytest-cov ; extra == 'dev'
   - pytest-timeout ; extra == 'dev'
@@ -3504,10 +3522,10 @@ packages:
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   requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/18/0e/a5f0257ab47492b7afb5fb60347d14ba19445e2773fc8352d4be6bd2f6f8/wcwidth-0.3.0-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/3c/c1/d73f12f8cdb1891334a2ccf7389eed244d3941e74d80dd220badb937f3fb/wcwidth-0.5.3-py3-none-any.whl
   name: wcwidth
-  version: 0.3.0
-  sha256: 073a1acb250e4add96cfd5ef84e0036605cd6e0d0782c8c15c80e42202348458
+  version: 0.5.3
+  sha256: d584eff31cd4753e1e5ff6c12e1edfdb324c995713f75d26c29807bb84bf649e
   requires_python: '>=3.8'
 - pypi: https://files.pythonhosted.org/packages/f4/24/2a3e3df732393fed8b3ebf2ec078f05546de641fe1b667ee316ec1dcf3b7/webencodings-0.5.1-py2.py3-none-any.whl
   name: webencodings
@@ -3523,14 +3541,15 @@ packages:
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   sha256: fd3cb4adb94a2a6e2b7c0d8d05cb94e6f1c81a0cf9dc2694fb65c7e8d94c42e4
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-- pypi: https://files.pythonhosted.org/packages/0b/2c/87f3254fd8ffd29e4c02732eee68a83a1d3c346ae39bc6822dcbcb697f2b/wheel-0.45.1-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/87/22/b76d483683216dde3d67cba61fb2444be8d5be289bf628c13fc0fd90e5f9/wheel-0.46.3-py3-none-any.whl
   name: wheel
-  version: 0.45.1
-  sha256: 708e7481cc80179af0e556bbf0cc00b8444c7321e2700b8d8580231d13017248
+  version: 0.46.3
+  sha256: 4b399d56c9d9338230118d705d9737a2a468ccca63d5e813e2a4fc7815d8bc4d
   requires_dist:
+  - packaging>=24.0
   - pytest>=6.0.0 ; extra == 'test'
-  - setuptools>=65 ; extra == 'test'
-  requires_python: '>=3.8'
+  - setuptools>=77 ; extra == 'test'
+  requires_python: '>=3.9'
 - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda
   sha256: 68f0206ca6e98fea941e5717cec780ed2873ffabc0e1ed34428c061e2c6268c7
   md5: 4a13eeac0b5c8e5b8ab496e6c4ddd829
diff --git a/pyproject.toml b/pyproject.toml
index 834c1e9..3854283 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,7 +24,7 @@ dependencies = [
   "sphinx-notfound-page>=1.1.0,<1.2.0",
   "sphinx-design>=0.6.1,<0.7",
   # autodoc
-  "openprotein-python>=0.10.0,<0.11.0",
+  "openprotein-python>=0.11.1,<0.12.0",
   "ipython>=9.8.0,<10",
 ]
 
@@ -44,6 +44,13 @@ build = "sphinx-build source build"
 dev = "sphinx-autobuild source build --port 5001"
 devinstall = "pip install -e ../openprotein-python-private"
 
+[tool.pixi.environments]
+dev = ["dev"]
+dev-nb = ["dev", "nb"]
+
+[tool.pixi.dependencies]
+pygments = ">=2.19.2,<3"
+
 [dependency-groups]
 dev = [
   "sphinx-autobuild",
@@ -57,14 +64,7 @@ dev = [
 nb = [
   "molviewspec",
   "ipykernel",
-  # "openprotein-python @ git+https://github.com/OpenProteinAI/openprotein-python-private.git@6e6214088bee247f20f72afe0bec4e8f686f08d9",
+  # "openprotein-python @ git+https://github.com/OpenProteinAI/openprotein-python-private.git@f2bd23a05b917c7e6edccd86a624f2f6cbb9f2a1",
   "seaborn",
   "scipy",
 ]
-
-[tool.pixi.environments]
-dev = ["dev"]
-dev-nb = ["dev", "nb"]
-
-[tool.pixi.dependencies]
-pygments = ">=2.19.2,<3"
diff --git a/source/_static/js/designSpec.js b/source/_static/js/designSpec.js
index 78d3c97..6dbfbde 100644
--- a/source/_static/js/designSpec.js
+++ b/source/_static/js/designSpec.js
@@ -3,7 +3,7 @@ const designSpec = {
   info: {
     title: "OpenProtein Design",
     description:
-      "# Design API\nThe Design API provided by OpenProtein.ai builds on top of our predictive models to empower you to achieve your protein design goals easily. \n\nCurrently, we support the following design algorithms:\n- **Genetic Algorithm** - Evolutionary optimization for sequence design using trained `predictors`\n- **RFdiffusion** - Diffusion-based structure generation for motif scaffolding, binder design, and symmetric assemblies\n- **BoltzGen** - Advanced diffusion model for protein structure and sequence design, supporting protein-ligand complexes, multi-chain assemblies, and cyclic peptides\n",
+      "# Design API\nThe Design API provided by OpenProtein.ai builds on top of our predictive models to empower you to achieve your protein design goals easily. \n\nCurrently, we support the following design algorithms:\n- **Genetic Algorithm** - Evolutionary optimization for sequence design\n- **RFdiffusion** - Diffusion-based structure generation for motif scaffolding, binder design, and symmetric assemblies\n- **BoltzGen** - Advanced diffusion model for protein structure and sequence design, supporting protein-ligand complexes, multi-chain assemblies, and cyclic peptides\n",
     version: "1.0.0",
   },
   paths: {
@@ -1216,7 +1216,7 @@ const designSpec = {
     "/api/v1/designer/design/{job_id}": {
       get: {
         tags: ["design"],
-        summary: "Get design metadata",
+        summary: "Get sequence optimization design metadata",
         description:
           "Get design job metadata.\n\nThis endpoint will be used after a successful POST request.",
         operationId: "getDesign",
@@ -1680,7 +1680,7 @@ const designSpec = {
     "/api/v1/designer/design/{job_id}/results": {
       get: {
         tags: ["design"],
-        summary: "Get design results",
+        summary: "Get sequence optimization design results",
         description:
           "Get design job with results if available.\n\nThis endpoint will be used after a successful POST request.",
         operationId: "getDesignResults",
@@ -2105,7 +2105,7 @@ const designSpec = {
               schema: {
                 title: "DesignRequestRFdiffusion",
                 description:
-                  "Request to design new structures using RFdiffusion.",
+                  "Request to design new structures using RFdiffusion.\n\n`query_id` or `contigs` is required.\n",
                 type: "object",
                 properties: {
                   n: {
@@ -2117,6 +2117,13 @@ const designSpec = {
                     example: 1,
                     "x-order": 101,
                   },
+                  query_id: {
+                    title: "Query ID",
+                    description:
+                      "ID of query which contains the encoded design request. This design request should be a partially/fully masked structure, which will be designed by the model. Either query_id or contigs should be specified.",
+                    type: "string",
+                    format: "uuid",
+                  },
                   structure_text: {
                     title: "Structure Text",
                     description: "String contents of the input PDB file.",
@@ -2250,6 +2257,10 @@ const designSpec = {
                   },
                 },
                 examples: {
+                  query: {
+                    n: 1,
+                    query_id: "afc17865-5c97-4b22-9c37-cdf3985e06bb",
+                  },
                   unconditional: {
                     n: 3,
                     contigs: "100-100",
@@ -2260,8 +2271,8 @@ const designSpec = {
                   },
                 },
                 example: {
-                  n: 3,
-                  contigs: "100-100",
+                  n: 1,
+                  query_id: "afc17865-5c97-4b22-9c37-cdf3985e06bb",
                 },
               },
             },
@@ -2512,9 +2523,9 @@ const designSpec = {
             "application/json": {
               schema: {
                 title: "DesignRequestBoltzGen",
-                description: "Request to design new structures using BoltzGen.",
+                description:
+                  "Request to design new structures using BoltzGen.\n\n`query_id` or `design_spec` is required.\n",
                 type: "object",
-                required: ["design_spec"],
                 properties: {
                   n: {
                     title: "Number of Designs",
@@ -2524,11 +2535,63 @@ const designSpec = {
                     example: 1,
                     "x-order": 101,
                   },
+                  query_id: {
+                    title: "Query ID",
+                    description:
+                      "ID of query which contains the encoded design request. This design request should be a partially/fully masked structure, which will be designed by the model. Either query_id or design_spec should be specified.",
+                    type: "string",
+                    format: "uuid",
+                  },
                   design_spec: {
-                    title: "Design Specification",
+                    title: "BoltzGenDesignSpec",
                     description:
-                      "BoltzGen design specification defining entities and constraints.",
-                    "x-order": 102,
+                      "Complete BoltzGen design specification including entities and constraints.",
+                    type: "object",
+                    required: ["entities"],
+                    properties: {
+                      entities: {
+                        title: "Entities",
+                        description:
+                          "List of entities in the design (proteins, ligands, or files).",
+                        type: "array",
+                        minItems: 1,
+                        items: {},
+                        "x-order": 1,
+                      },
+                      constraints: {
+                        title: "Constraints",
+                        description: "List of constraints for the design.",
+                        type: "array",
+                        nullable: true,
+                        default: null,
+                        items: {},
+                        "x-order": 2,
+                      },
+                    },
+                    example: {
+                      entities: [
+                        {
+                          protein: {
+                            id: "A",
+                            sequence: "ACDEFGHIKLMNPQRSTVWY",
+                          },
+                        },
+                        {
+                          ligand: {
+                            id: "B",
+                            ccd: "ATP",
+                          },
+                        },
+                      ],
+                      constraints: [
+                        {
+                          bond: {
+                            atom1: ["A", 10, "CA"],
+                            atom2: ["B", 1, "O"],
+                          },
+                        },
+                      ],
+                    },
                   },
                   structure_text: {
                     title: "Structure Text",
@@ -2575,6 +2638,10 @@ const designSpec = {
                   },
                 },
                 examples: {
+                  query: {
+                    n: 1,
+                    query_id: "afc17865-5c97-4b22-9c37-cdf3985e06bb",
+                  },
                   unconditional: {
                     design_spec: {
                       entities: [
@@ -2636,16 +2703,7 @@ const designSpec = {
                 },
                 example: {
                   n: 1,
-                  design_spec: {
-                    entities: [
-                      {
-                        protein: {
-                          id: "A",
-                          sequence: "100",
-                        },
-                      },
-                    ],
-                  },
+                  query_id: "afc17865-5c97-4b22-9c37-cdf3985e06bb",
                 },
               },
             },
@@ -3042,6 +3100,140 @@ const designSpec = {
         ],
       },
     },
+    "/api/v1/design/{job_id}/results": {
+      get: {
+        tags: ["structure generation"],
+        summary: "Retrieve structure generation result",
+        description: "Get designed structure for a submitted design sequence",
+        parameters: [
+          {
+            name: "job_id",
+            in: "path",
+            description: "Job ID to fetch",
+            required: true,
+            schema: {
+              type: "string",
+              format: "uuid",
+            },
+          },
+          {
+            name: "replicate",
+            in: "query",
+            description:
+              "Replicate index out of the `N` requested designs. Defaults to the first design.\n",
+            required: false,
+            schema: {
+              type: "integer",
+              default: 0,
+            },
+          },
+          {
+            name: "format",
+            in: "query",
+            description:
+              "Output format to retrieve the result in.\n\nDefaults to `pdb`. Note that requested format may not be supported for all jobs depending on when the job was created.\n",
+            required: false,
+            schema: {
+              title: "OutputFormat",
+              description:
+                "Output format of folded structure. Defaults to pdb.",
+              type: "string",
+              enum: ["pdb", "mmcif"],
+              default: "pdb",
+            },
+          },
+        ],
+        responses: {
+          "200": {
+            description: "Result encoded in requested format.",
+            content: {
+              "chemical/x-mmcif": {
+                schema: {
+                  title: "CIFOutput",
+                  description: "An output CIF structure file.",
+                  type: "string",
+                  example:
+                    'data_example\n#\n_entry.id   example\n#\nloop_\n_entity.id\n_entity.type\n_entity.pdbx_description\n1 polymer "Example protein chain"\n#\nloop_\n_atom_site.group_PDB\n_atom_site.id\n_atom_site.type_symbol\n_atom_site.label_atom_id\n_atom_site.label_comp_id\n_atom_site.label_asym_id\n_atom_site.label_entity_id\n_atom_site.label_seq_id\n_atom_site.Cartn_x\n_atom_site.Cartn_y\n_atom_site.Cartn_z\nATOM 1 N N MET A 1 1 12.011 13.456 14.789\nATOM 2 C CA MET A 1 1 13.123 14.567 15.890\nATOM 3 C C MET A 1 1 14.234 15.678 16.901\nATOM 4 O O MET A 1 1 15.345 16.789 17.012\n#\n',
+                },
+              },
+              "chemical/x-pdb": {
+                schema: {
+                  title: "PDBOutput",
+                  description: "An output pdb structure file.",
+                  type: "string",
+                  example:
+                    "HEADER    OXYGEN TRANSPORT                         29-JUL-76   1HHO              \nTITLE     DEOXY HUMAN HEMOGLOBIN                                                \nCOMPND    MOL_ID: 1; MOLECULE: HEMOGLOBIN; CHAIN: A, B, C, D;                   \nSOURCE    HUMAN (HOMO SAPIENS)                                                   \nKEYWDS    OXYGEN TRANSPORT, HEME                                                 \nEXPDTA    X-RAY DIFFRACTION                                                     \nAUTHOR    F.PERUTZ,R.MATTHEWS                                                    \nREVDAT   1   24-FEB-09 1HHO    0                                                \nSEQRES   1 A   141  VAL LEU SER PRO ALA ASP LYS THR VAL LEU THR PRO GLU GLU     \nSEQRES   2 A   141  LYS SER ALA GLY PHE LEU SER PRO GLU GLY ALA GLY\n",
+                },
+              },
+            },
+          },
+          "400": {
+            description:
+              "Result retrieval error. Contact support for assistance if persistent.",
+            content: {
+              "application/json": {
+                schema: {
+                  title: "Error",
+                  description: "A error object providing details of the error.",
+                  required: ["detail"],
+                  type: "object",
+                  properties: {
+                    detail: {
+                      title: "Detail",
+                      type: "string",
+                    },
+                  },
+                },
+              },
+            },
+          },
+          "401": {
+            description:
+              "Bad or expired token. This can happen if the token is revoked or expired. User should re-authenticate with their credentials.",
+            content: {
+              "application/json": {
+                schema: {
+                  title: "Error",
+                  description: "A error object providing details of the error.",
+                  required: ["detail"],
+                  type: "object",
+                  properties: {
+                    detail: {
+                      title: "Detail",
+                      type: "string",
+                    },
+                  },
+                },
+              },
+            },
+          },
+          "404": {
+            description: "Fold job not found.",
+            content: {
+              "application/json": {
+                schema: {
+                  title: "Error",
+                  description: "A error object providing details of the error.",
+                  required: ["detail"],
+                  type: "object",
+                  properties: {
+                    detail: {
+                      title: "Detail",
+                      type: "string",
+                    },
+                  },
+                },
+              },
+            },
+          },
+        },
+        security: [
+          {
+            oauth2: [],
+          },
+        ],
+      },
+    },
   },
   components: {
     securitySchemes: {
@@ -3049,7 +3241,7 @@ const designSpec = {
         type: "oauth2",
         flows: {
           password: {
-            tokenUrl: "/api/v1/login/access-token",
+            tokenUrl: "/api/v1/auth/login",
             scopes: {},
           },
         },
@@ -4372,7 +4564,8 @@ const designSpec = {
       },
       DesignRequestRFdiffusion: {
         title: "DesignRequestRFdiffusion",
-        description: "Request to design new structures using RFdiffusion.",
+        description:
+          "Request to design new structures using RFdiffusion.\n\n`query_id` or `contigs` is required.\n",
         type: "object",
         properties: {
           n: {
@@ -4384,6 +4577,13 @@ const designSpec = {
             example: 1,
             "x-order": 101,
           },
+          query_id: {
+            title: "Query ID",
+            description:
+              "ID of query which contains the encoded design request. This design request should be a partially/fully masked structure, which will be designed by the model. Either query_id or contigs should be specified.",
+            type: "string",
+            format: "uuid",
+          },
           structure_text: {
             title: "Structure Text",
             description: "String contents of the input PDB file.",
@@ -4515,6 +4715,10 @@ const designSpec = {
           },
         },
         examples: {
+          query: {
+            n: 1,
+            query_id: "afc17865-5c97-4b22-9c37-cdf3985e06bb",
+          },
           unconditional: {
             n: 3,
             contigs: "100-100",
@@ -4525,15 +4729,66 @@ const designSpec = {
           },
         },
         example: {
-          n: 3,
-          contigs: "100-100",
+          n: 1,
+          query_id: "afc17865-5c97-4b22-9c37-cdf3985e06bb",
+        },
+      },
+      BoltzGenDesignSpec: {
+        title: "BoltzGenDesignSpec",
+        description:
+          "Complete BoltzGen design specification including entities and constraints.",
+        type: "object",
+        required: ["entities"],
+        properties: {
+          entities: {
+            title: "Entities",
+            description:
+              "List of entities in the design (proteins, ligands, or files).",
+            type: "array",
+            minItems: 1,
+            items: {},
+            "x-order": 1,
+          },
+          constraints: {
+            title: "Constraints",
+            description: "List of constraints for the design.",
+            type: "array",
+            nullable: true,
+            default: null,
+            items: {},
+            "x-order": 2,
+          },
+        },
+        example: {
+          entities: [
+            {
+              protein: {
+                id: "A",
+                sequence: "ACDEFGHIKLMNPQRSTVWY",
+              },
+            },
+            {
+              ligand: {
+                id: "B",
+                ccd: "ATP",
+              },
+            },
+          ],
+          constraints: [
+            {
+              bond: {
+                atom1: ["A", 10, "CA"],
+                atom2: ["B", 1, "O"],
+              },
+            },
+          ],
         },
       },
       DesignRequestBoltzGen: {
         title: "DesignRequestBoltzGen",
-        description: "Request to design new structures using BoltzGen.",
+        description:
+          "Request to design new structures using BoltzGen.\n\n`query_id` or `design_spec` is required.\n",
         type: "object",
-        required: ["design_spec"],
         properties: {
           n: {
             title: "Number of Designs",
@@ -4543,11 +4798,63 @@ const designSpec = {
             example: 1,
             "x-order": 101,
           },
+          query_id: {
+            title: "Query ID",
+            description:
+              "ID of query which contains the encoded design request. This design request should be a partially/fully masked structure, which will be designed by the model. Either query_id or design_spec should be specified.",
+            type: "string",
+            format: "uuid",
+          },
           design_spec: {
-            title: "Design Specification",
+            title: "BoltzGenDesignSpec",
             description:
-              "BoltzGen design specification defining entities and constraints.",
-            "x-order": 102,
+              "Complete BoltzGen design specification including entities and constraints.",
+            type: "object",
+            required: ["entities"],
+            properties: {
+              entities: {
+                title: "Entities",
+                description:
+                  "List of entities in the design (proteins, ligands, or files).",
+                type: "array",
+                minItems: 1,
+                items: {},
+                "x-order": 1,
+              },
+              constraints: {
+                title: "Constraints",
+                description: "List of constraints for the design.",
+                type: "array",
+                nullable: true,
+                default: null,
+                items: {},
+                "x-order": 2,
+              },
+            },
+            example: {
+              entities: [
+                {
+                  protein: {
+                    id: "A",
+                    sequence: "ACDEFGHIKLMNPQRSTVWY",
+                  },
+                },
+                {
+                  ligand: {
+                    id: "B",
+                    ccd: "ATP",
+                  },
+                },
+              ],
+              constraints: [
+                {
+                  bond: {
+                    atom1: ["A", 10, "CA"],
+                    atom2: ["B", 1, "O"],
+                  },
+                },
+              ],
+            },
           },
           structure_text: {
             title: "Structure Text",
@@ -4594,6 +4901,10 @@ const designSpec = {
           },
         },
         examples: {
+          query: {
+            n: 1,
+            query_id: "afc17865-5c97-4b22-9c37-cdf3985e06bb",
+          },
           unconditional: {
             design_spec: {
               entities: [
@@ -4655,16 +4966,7 @@ const designSpec = {
         },
         example: {
           n: 1,
-          design_spec: {
-            entities: [
-              {
-                protein: {
-                  id: "A",
-                  sequence: "100",
-                },
-              },
-            ],
-          },
+          query_id: "afc17865-5c97-4b22-9c37-cdf3985e06bb",
         },
       },
       StructureGenerate: {
@@ -4754,6 +5056,27 @@ const designSpec = {
           },
         },
       },
+      OutputFormat: {
+        title: "OutputFormat",
+        description: "Output format of folded structure. Defaults to pdb.",
+        type: "string",
+        enum: ["pdb", "mmcif"],
+        default: "pdb",
+      },
+      CIFOutput: {
+        title: "CIFOutput",
+        description: "An output CIF structure file.",
+        type: "string",
+        example:
+          'data_example\n#\n_entry.id   example\n#\nloop_\n_entity.id\n_entity.type\n_entity.pdbx_description\n1 polymer "Example protein chain"\n#\nloop_\n_atom_site.group_PDB\n_atom_site.id\n_atom_site.type_symbol\n_atom_site.label_atom_id\n_atom_site.label_comp_id\n_atom_site.label_asym_id\n_atom_site.label_entity_id\n_atom_site.label_seq_id\n_atom_site.Cartn_x\n_atom_site.Cartn_y\n_atom_site.Cartn_z\nATOM 1 N N MET A 1 1 12.011 13.456 14.789\nATOM 2 C CA MET A 1 1 13.123 14.567 15.890\nATOM 3 C C MET A 1 1 14.234 15.678 16.901\nATOM 4 O O MET A 1 1 15.345 16.789 17.012\n#\n',
+      },
+      PDBOutput: {
+        title: "PDBOutput",
+        description: "An output pdb structure file.",
+        type: "string",
+        example:
+          "HEADER    OXYGEN TRANSPORT                         29-JUL-76   1HHO              \nTITLE     DEOXY HUMAN HEMOGLOBIN                                                \nCOMPND    MOL_ID: 1; MOLECULE: HEMOGLOBIN; CHAIN: A, B, C, D;                   \nSOURCE    HUMAN (HOMO SAPIENS)                                                   \nKEYWDS    OXYGEN TRANSPORT, HEME                                                 \nEXPDTA    X-RAY DIFFRACTION                                                     \nAUTHOR    F.PERUTZ,R.MATTHEWS                                                    \nREVDAT   1   24-FEB-09 1HHO    0                                                \nSEQRES   1 A   141  VAL LEU SER PRO ALA ASP LYS THR VAL LEU THR PRO GLU GLU     \nSEQRES   2 A   141  LYS SER ALA GLY PHE LEU SER PRO GLU GLY ALA GLY\n",
+      },
     },
   },
   tags: [
diff --git a/source/_static/js/foldSpec.js b/source/_static/js/foldSpec.js
index 2ba4241..95fb9de 100644
--- a/source/_static/js/foldSpec.js
+++ b/source/_static/js/foldSpec.js
@@ -3933,7 +3933,7 @@ const foldSpec = {
         ],
       },
     },
-    "/api/v1/fold/{job_id}/{sequence}": {
+    "/api/v1/fold/{job_id}/{index}": {
       get: {
         tags: ["fold"],
         summary: "Retrieve protein structure",
@@ -3950,12 +3950,12 @@ const foldSpec = {
             },
           },
           {
-            name: "sequence",
+            name: "index",
             in: "path",
-            description: "Sequence for which to retrieve result",
+            description: "Index of batch for which to retrieve result",
             required: true,
             schema: {
-              type: "string",
+              type: "number",
             },
           },
           {
@@ -4065,11 +4065,11 @@ const foldSpec = {
         ],
       },
     },
-    "/api/v1/fold/{job_id}/complex": {
+    "/api/v1/fold/{job_id}/{index}/{extraKey}": {
       get: {
         tags: ["fold"],
-        summary: "Retrieve protein complex structure",
-        description: "Get protein complex structure for a submitted sequence",
+        summary: "Retrieve extra result",
+        description: "Get protein structure for a submitted sequence",
         parameters: [
           {
             name: "job_id",
@@ -4082,41 +4082,43 @@ const foldSpec = {
             },
           },
           {
-            name: "format",
-            in: "query",
-            description:
-              "Output format to retrieve the result in.\n\nDefaults to `pdb`. Note that requested format may not be supported for all jobs depending on when the job was created.\n",
-            required: false,
+            name: "index",
+            in: "path",
+            description: "Index of batch for which to retrieve result",
+            required: true,
+            schema: {
+              type: "number",
+            },
+          },
+          {
+            name: "extraKey",
+            in: "path",
+            description: "Extra key for extra result provided by fold model",
+            required: true,
             schema: {
-              title: "OutputFormat",
-              description:
-                "Output format of folded structure. Defaults to pdb.",
               type: "string",
-              enum: ["pdb", "mmcif"],
-              default: "pdb",
+              enum: [
+                "pae",
+                "pde",
+                "plddt",
+                "ptm",
+                "confidence",
+                "affinity",
+                "score",
+                "metrics",
+              ],
             },
           },
         ],
         responses: {
           "200": {
-            description: "Result encoded in mmCIF/PDB.",
+            description:
+              "Extra result which could be a numpy array, or json, or csv.\n\npae, pde, plddt, ptm returns a .npy.\nconfidence, affinity returns a json.\nscore, metrics returns a csv.\n",
             content: {
-              "chemical/x-mmcif": {
-                schema: {
-                  title: "CIFOutput",
-                  description: "An output CIF structure file.",
-                  type: "string",
-                  example:
-                    'data_example\n#\n_entry.id   example\n#\nloop_\n_entity.id\n_entity.type\n_entity.pdbx_description\n1 polymer "Example protein chain"\n#\nloop_\n_atom_site.group_PDB\n_atom_site.id\n_atom_site.type_symbol\n_atom_site.label_atom_id\n_atom_site.label_comp_id\n_atom_site.label_asym_id\n_atom_site.label_entity_id\n_atom_site.label_seq_id\n_atom_site.Cartn_x\n_atom_site.Cartn_y\n_atom_site.Cartn_z\nATOM 1 N N MET A 1 1 12.011 13.456 14.789\nATOM 2 C CA MET A 1 1 13.123 14.567 15.890\nATOM 3 C C MET A 1 1 14.234 15.678 16.901\nATOM 4 O O MET A 1 1 15.345 16.789 17.012\n#\n',
-                },
-              },
-              "chemical/x-pdb": {
+              "application/octet-stream": {
                 schema: {
-                  title: "PDBOutput",
-                  description: "An output pdb structure file.",
-                  type: "string",
-                  example:
-                    "HEADER    OXYGEN TRANSPORT                         29-JUL-76   1HHO              \nTITLE     DEOXY HUMAN HEMOGLOBIN                                                \nCOMPND    MOL_ID: 1; MOLECULE: HEMOGLOBIN; CHAIN: A, B, C, D;                   \nSOURCE    HUMAN (HOMO SAPIENS)                                                   \nKEYWDS    OXYGEN TRANSPORT, HEME                                                 \nEXPDTA    X-RAY DIFFRACTION                                                     \nAUTHOR    F.PERUTZ,R.MATTHEWS                                                    \nREVDAT   1   24-FEB-09 1HHO    0                                                \nSEQRES   1 A   141  VAL LEU SER PRO ALA ASP LYS THR VAL LEU THR PRO GLU GLU     \nSEQRES   2 A   141  LYS SER ALA GLY PHE LEU SER PRO GLU GLY ALA GLY\n",
+                  type: "binary",
+                  description: "Extra result as a file.",
                 },
               },
             },
diff --git a/source/python-api/api-reference/molecules.rst b/source/python-api/api-reference/molecules.rst
index 4559beb..0e42711 100644
--- a/source/python-api/api-reference/molecules.rst
+++ b/source/python-api/api-reference/molecules.rst
@@ -50,3 +50,11 @@ RNA
 
 .. autoclass:: openprotein.molecules.RNA
    :members:
+
+Template
+^^^^^^^^
+
+:py:class:`~openprotein.molecules.Template` describes a template that can be used for constraining fold jobs.
+
+.. autoclass:: openprotein.molecules.Template
+   :members:
diff --git a/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb b/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb
index c168d92..4a0764d 100644
--- a/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb
+++ b/source/walkthroughs/Nanobody_binder_design_with_BoltzGen.ipynb
@@ -33,7 +33,7 @@
     "To run this tutorial, you'll need a Python environment containing the following\n",
     "packages:\n",
     "\n",
-    "- `openprotein_python>=0.10.1`\n",
+    "- `openprotein_python>=0.11.0`\n",
     "- `molviewspec` (for structure visualization)\n",
     "\n",
     "See the Python client [installation instructions](../python-api/installation.html) for more info.\n",
@@ -890,23 +890,19 @@
     "\n",
     "Typically, to validate *in silico* binder designs, we predict the target-binder complex\n",
     "structure and check for consistency with the original designed structure and binding\n",
-    "interface. Because the structure of the  target is known, but the binder structure is\n",
+    "interface. Because the structure of the target is known, but the binder structure is\n",
     "not, we usually run structure prediction in single sequence mode for both the binder and\n",
     "target sequences using only the target structure as a template. _Single sequence mode_\n",
     "means that no multiple sequence alignment is used for the binder. This is important to\n",
     "efficiently screen large numbers of binder designs where homology search is a bottleneck.\n",
     "\n",
-    "However, because we do support templates yet (coming soon!), in this tutorial we'll\n",
-    "use an MSA for the target instead of a template; this generally achieves the same\n",
-    "objective, allowing the model to accurately recapitulate the target's known structure.\n",
-    "\n",
-    "Below, we compute an MSA for the target, and use it to predict the structure of all\n",
-    "designed sequences; this generally takes about 50 minutes."
+    "Below, we apply this approach to predict the structures of all designed sequences; this\n",
+    "generally takes about 50 minutes."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": null,
    "id": "78ea020d",
    "metadata": {},
    "outputs": [
@@ -926,29 +922,28 @@
     }
    ],
    "source": [
-    "# 1. Compute MSA for target to use for folding\n",
-    "target_msa = session.align.create_msa(target.sequence)\n",
-    "\n",
-    "# 2. Create the complexes to fold\n",
+    "# 1. Create the complexes to fold\n",
     "complexes_to_fold = []\n",
     "for i, generated_structure in enumerate(generated_structures):  # for each structure\n",
     "    for j in range(N_SEQS_PER_STRUCTURE):\n",
     "        designed_binder_sequence = df.loc[(i, j)][\"sequence\"]\n",
+    "        # 1a. Create the complex to fold, containing the target sequence and designed\n",
+    "        #     binder sequence\n",
     "        complex = Complex(\n",
     "            {\"A\": Protein(target.sequence), \"B\": Protein(designed_binder_sequence)}\n",
     "        )\n",
-    "        # set MSAs to use for structure prediction\n",
-    "        #   note that `binder.msa = Protein.single_sequence_mode` needs to be set\n",
-    "        #   explicitly when running structure prediction without MSAs\n",
-    "        complex.get_protein(chain_id=\"A\").msa = target_msa\n",
+    "        # 1b. Set both the target MSA and the binder MSA to single sequence mode\n",
+    "        complex.get_protein(chain_id=\"A\").msa = Protein.single_sequence_mode\n",
     "        complex.get_protein(chain_id=\"B\").msa = Protein.single_sequence_mode\n",
+    "        # 1c. Set the known target structure as a template for the target only\n",
+    "        complex.get_protein(chain_id=\"A\").templates = [target]\n",
     "        complexes_to_fold.append(complex)\n",
     "\n",
-    "# 3. Create the job\n",
+    "# 2. Create the job\n",
     "fold_job = session.fold.boltz_2.fold(complexes_to_fold)\n",
     "print(fold_job)\n",
     "\n",
-    "# 4. Wait for the job to finish\n",
+    "# 3. Wait for the job to finish\n",
     "_ = fold_job.wait_until_done(verbose=True)"
    ]
   },
@@ -1281,8 +1276,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "# designs passing filters 250\n",
-      "# unique structures passing filters 77\n"
+      "# designs passing filters 146\n",
+      "# unique structures passing filters 48\n"
      ]
     }
    ],
@@ -1484,7 +1479,7 @@
     "]\n",
     "predicted_structure = predicted_structures[design_idx]\n",
     "generated_structure = generated_structures[structure_idx]\n",
-    "# superimpose predicted structure on the generate structure\n",
+    "# superimpose predicted structure on the generated structure\n",
     "predicted_structure = predicted_structure.copy().superimpose_onto(generated_structure)\n",
     "# visualize\n",
     "visualize_cif(\n",
@@ -1549,7 +1544,7 @@
     "]\n",
     "predicted_structure = predicted_structures[design_idx]\n",
     "generated_structure = generated_structures[structure_idx]\n",
-    "# superimpose predicted structure on the generate structure\n",
+    "# superimpose predicted structure on the generated structure\n",
     "predicted_structure = predicted_structure.copy().superimpose_onto(generated_structure)\n",
     "# visualize\n",
     "visualize_cif(\n",
diff --git a/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb b/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb
index 1ae9b9c..feb6305 100644
--- a/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb
+++ b/source/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.ipynb
@@ -38,7 +38,7 @@
     "To run this tutorial, you'll need a Python environment containing the following\n",
     "packages:\n",
     "\n",
-    "- `openprotein_python>=0.10`\n",
+    "- `openprotein_python>=0.10.2`\n",
     "- `molviewspec` (for structure visualization)\n",
     "\n",
     "See the Python client [installation instructions](../python-api/installation.html) for more info.\n",
@@ -1312,18 +1312,14 @@
     "\n",
     "Typically, to validate *in silico* binder designs, we predict the target-binder complex\n",
     "structure and check for consistency with the original designed structure and binding\n",
-    "interface. Because the structure of the  target is known, but the binder structure is\n",
+    "interface. Because the structure of the target is known, but the binder structure is\n",
     "not, we usually run structure prediction in single sequence mode for both the binder and\n",
     "target sequences using only the target structure as a template. _Single sequence mode_\n",
     "means that no multiple sequence alignment is used for the binder. This is important to\n",
     "efficiently screen large numbers of binder designs where homology search is a bottleneck.\n",
     "\n",
-    "However, because we do support templates yet (coming soon!), in this tutorial we'll\n",
-    "use an MSA for the target instead of a template; this generally achieves the same\n",
-    "objective, allowing the model to accurately recapitulate the target's known structure.\n",
-    "\n",
-    "Below, we compute an MSA for the target, and use it to predict the structure of all\n",
-    "designed sequences; this generally takes about 50 minutes."
+    "Below, we apply this approach to predict the structures of all designed sequences; this\n",
+    "generally takes about 50 minutes."
    ]
   },
   {
@@ -1348,29 +1344,28 @@
     }
    ],
    "source": [
-    "# 1. Compute MSA for target to use for folding\n",
-    "target_msa = session.align.create_msa(target.sequence)\n",
-    "\n",
-    "# 2. Create the complexes to fold\n",
+    "# 1. Create the complexes to fold\n",
     "complexes_to_fold = []\n",
     "for i, generated_structure in enumerate(generated_structures):  # for each structure\n",
     "    for j in range(N_SEQS_PER_STRUCTURE):\n",
     "        designed_binder_sequence = df.loc[(i, j)][\"sequence\"]\n",
+    "        # 1a. Create the complex to fold, containing the target sequence and designed\n",
+    "        #     binder sequence\n",
     "        complex = Complex(\n",
     "            {\"A\": Protein(target.sequence), \"B\": Protein(designed_binder_sequence)}\n",
     "        )\n",
-    "        # set MSAs to use for structure prediction\n",
-    "        #   note that `binder.msa = Protein.single_sequence_mode` needs to be set\n",
-    "        #   explicitly when running structure prediction without MSAs\n",
-    "        complex.get_protein(chain_id=\"A\").msa = target_msa\n",
+    "        # 1b. Set both the target MSA and the binder MSA to single sequence mode\n",
+    "        complex.get_protein(chain_id=\"A\").msa = Protein.single_sequence_mode\n",
     "        complex.get_protein(chain_id=\"B\").msa = Protein.single_sequence_mode\n",
+    "        # 1c. Set the known target structure as a template for the target only\n",
+    "        complex.get_protein(chain_id=\"A\").templates = [target]\n",
     "        complexes_to_fold.append(complex)\n",
     "\n",
-    "# 3. Create the job\n",
+    "# 2. Create the job\n",
     "fold_job = session.fold.boltz_2.fold(complexes_to_fold)\n",
     "print(fold_job)\n",
     "\n",
-    "# 4. Wait for the job to finish\n",
+    "# 3. Wait for the job to finish\n",
     "_ = fold_job.wait_until_done(verbose=True)"
    ]
   },
@@ -1720,8 +1715,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "# designs passing filters 279\n",
-      "# unique structures passing filters 65\n"
+      "# designs passing filters 253\n",
+      "# unique structures passing filters 58\n"
      ]
     }
    ],
@@ -1945,7 +1940,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 47,
+   "execution_count": null,
    "id": "3816751b",
    "metadata": {},
    "outputs": [
@@ -1974,10 +1969,12 @@
    ],
    "source": [
     "# get predicted and generated structure of top design\n",
-    "design_idx, structure_idx = 263, 26\n",
+    "design_idx, structure_idx = df_selected.reset_index().iloc[0][\n",
+    "    [\"design_idx\", \"structure_idx\"]\n",
+    "]\n",
     "predicted_structure = predicted_structures[design_idx]\n",
     "generated_structure = generated_structures[structure_idx]\n",
-    "# superimpose predicted structure on the generate structure\n",
+    "# superimpose predicted structure on the generated structure\n",
     "predicted_structure = predicted_structure.copy().superimpose_onto(generated_structure)\n",
     "# visualize\n",
     "visualize_cif(\n",
@@ -2016,7 +2013,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 48,
+   "execution_count": null,
    "id": "87fde147",
    "metadata": {},
    "outputs": [
@@ -2045,10 +2042,12 @@
    ],
    "source": [
     "# get predicted and generated structure of top sixth design\n",
-    "design_idx, structure_idx = 530, 53\n",
+    "design_idx, structure_idx = df_selected.reset_index().iloc[5][\n",
+    "    [\"design_idx\", \"structure_idx\"]\n",
+    "]\n",
     "predicted_structure = predicted_structures[design_idx]\n",
     "generated_structure = generated_structures[structure_idx]\n",
-    "# superimpose predicted structure on the generate structure\n",
+    "# superimpose predicted structure on the generated structure\n",
     "predicted_structure = predicted_structure.copy().superimpose_onto(generated_structure)\n",
     "# visualize\n",
     "visualize_cif(\n",