From d920464e5b8413fc6a6fab1be1cd7c5e03309595 Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Fri, 6 Nov 2026 13:40:18 +0100
Subject: [PATCH 01/11] Rename all cookbook links to how-to guides

---
 abfe_tutorial/abfe_tutorial.ipynb             |  2 +-
 ahfe_tutorial/ahfe_tutorial.ipynb             |  2 +-
 cookbook/cofactors_rbfe.ipynb                 |  6 +++---
 cookbook/create_alchemical_network.ipynb      | 20 +++++++++----------
 cookbook/generate_ligand_network.ipynb        |  6 +++---
 cookbook/hand_write_ligand_network.ipynb      | 12 +++++------
 cookbook/ligandnetwork_vis.ipynb              |  2 +-
 cookbook/loading_molecules.ipynb              |  2 +-
 cookbook/network_from_orion_fepp.ipynb        |  8 ++++----
 cookbook/repairing_broken_networks.ipynb      |  2 +-
 cookbook/rfe_alchemical_planners.ipynb        |  2 +-
 cookbook/user_charges.ipynb                   |  4 ++--
 .../task_based_execution_python_api.ipynb     |  4 ++--
 openmm_md/plain_md.ipynb                      |  2 +-
 openmm_septop/septop_tutorial.ipynb           |  2 +-
 rbfe_tutorial/rbfe_python_tutorial.ipynb      |  2 +-
 showcase/openfe_showcase.ipynb                | 16 ++++-----------
 17 files changed, 43 insertions(+), 51 deletions(-)

diff --git a/abfe_tutorial/abfe_tutorial.ipynb b/abfe_tutorial/abfe_tutorial.ipynb
index 4f47a51f..d6f21af8 100644
--- a/abfe_tutorial/abfe_tutorial.ipynb
+++ b/abfe_tutorial/abfe_tutorial.ipynb
@@ -130,7 +130,7 @@
     "\n",
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
-    "**Learn more:** To assign partial charges to your own ligands, see the cookbook on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/cookbook/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
+    "**Learn more:** To assign partial charges to your own ligands, see the How-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
     "\n",
     "</div>"
    ]
diff --git a/ahfe_tutorial/ahfe_tutorial.ipynb b/ahfe_tutorial/ahfe_tutorial.ipynb
index 421155a9..bca79595 100644
--- a/ahfe_tutorial/ahfe_tutorial.ipynb
+++ b/ahfe_tutorial/ahfe_tutorial.ipynb
@@ -122,7 +122,7 @@
    "source": [
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
-    "**Partial charges:** The ligand in `benzene_am1bcc.sdf` already has AM1-BCC partial charges, so the same charges are used in every repeat. To assign partial charges to your own ligands, see the cookbook on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/cookbook/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
+    "**Partial charges:** The ligand in `benzene_am1bcc.sdf` already has AM1-BCC partial charges, so the same charges are used in every repeat. To assign partial charges to your own ligands, see the How-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
     "\n",
     "</div>"
    ]
diff --git a/cookbook/cofactors_rbfe.ipynb b/cookbook/cofactors_rbfe.ipynb
index c495c018..602a167b 100644
--- a/cookbook/cofactors_rbfe.ipynb
+++ b/cookbook/cofactors_rbfe.ipynb
@@ -7,7 +7,7 @@
    "source": [
     "# Defining Cofactors\n",
     "\n",
-    "This cookbook demonstrates how to define cofactors (any small molecules that are not the bound ligand) with 1) the ``openfe`` CLI during the planning phase and 2) directly using the Python API.\n",
+    "This How-to guide demonstrates how to define cofactors (any small molecules that are not the bound ligand) with 1) the ``openfe`` CLI during the planning phase and 2) directly using the Python API.\n",
     "\n",
     "Similar to `ligand` definition, `cofactors` can be loaded from in SDF file format, and multiple molecules can be defined in a single file."
    ]
@@ -65,7 +65,7 @@
     "\n",
     "\n",
     "<div class=\"alert alert-warning\">\n",
-    "Note that partial charges are already assigned for both the ligands and cofactors. See <a href=\"https://docs.openfree.energy/en/latest/cookbook/user_charges.html\">Assigning partial charges to an OpenFF Molecule</a> or and <a href=\" https://docs.openfree.energy/en/latest/reference/cli/charge_molecules.html\">charge-molecules CLI command</a> for information on assigning partial charges.\n",
+    "Note that partial charges are already assigned for both the ligands and cofactors. See <a href=\"https://docs.openfree.energy/en/latest/how_to_guides/user_charges.html\">Assigning partial charges to an OpenFF Molecule</a> or and <a href=\" https://docs.openfree.energy/en/latest/reference/cli/charge_molecules.html\">charge-molecules CLI command</a> for information on assigning partial charges.\n",
     "\n",
     "Supplying cofactors as SmallMoleculeCompoents means they will be parameterized using the small molecule force field, which might not be applicable in all situations.\n",
     "</div>\n"
@@ -359,7 +359,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.13.11"
+   "version": "3.13.14"
   }
  },
  "nbformat": 4,
diff --git a/cookbook/create_alchemical_network.ipynb b/cookbook/create_alchemical_network.ipynb
index 2803edcf..a38d18a2 100644
--- a/cookbook/create_alchemical_network.ipynb
+++ b/cookbook/create_alchemical_network.ipynb
@@ -51,8 +51,8 @@
    "id": "6bfee4c7-0aaf-49a6-b35a-bdbe99444bab",
    "metadata": {},
    "source": [
-    "This cookbook assumes you've already loaded a `LigandNetwork`.\n",
-    "To learn how to build a `LigandNetwork`, see [Planning a Ligand Network](https://docs.openfree.energy/en/stable/cookbook/generate_ligand_network.html)."
+    "This How-to guide assumes you've already loaded a `LigandNetwork`.\n",
+    "To learn how to build a `LigandNetwork`, see [Planning a Ligand Network](https://docs.openfree.energy/en/stable/how_to_guides/generate_ligand_network.html)."
    ]
   },
   {
@@ -85,7 +85,7 @@
    "source": [
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
-    "**Partial charges:** The ligands in `somebenzenes_am1bcc.sdf` already have AM1-BCC partial charges, so the same charges are used in every repeat. To assign partial charges to your own ligands, see the cookbook on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/cookbook/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
+    "**Partial charges:** The ligands in `somebenzenes_am1bcc.sdf` already have AM1-BCC partial charges, so the same charges are used in every repeat. To assign partial charges to your own ligands, see the How-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
     "\n",
     "</div>"
    ]
@@ -95,9 +95,9 @@
    "id": "405fe819-b4a6-408b-8623-041492c84dfb",
    "metadata": {},
    "source": [
-    "This cookbook assumes you've already loaded a `Protocol`. For more information, see [Choose and Configure a Protocol]:\n",
+    "This How-to guide assumes you've already loaded a `Protocol`. For more information, see [Choose and Configure a Protocol]:\n",
     "\n",
-    "[Choose and Configure a Protocol]: https://docs.openfree.energy/en/stable/cookbook/choose_protocol.html"
+    "[Choose and Configure a Protocol]: https://docs.openfree.energy/en/stable/how_to_guides/choose_protocol.html"
    ]
   },
   {
@@ -117,9 +117,9 @@
    "id": "0908d2b2-421d-4b51-8b35-d2cca5e25a95",
    "metadata": {},
    "source": [
-    "This cookbook assumes you've already loaded a solvent and all the other chemical components of the system, including any proteins or cofactors. For more information, see [Loading your data into Components]:\n",
+    "This How-to guide assumes you've already loaded a solvent and all the other chemical components of the system, including any proteins or cofactors. For more information, see [Loading your data into Components]:\n",
     "\n",
-    "[Loading your data into Components]: https://docs.openfree.energy/en/stable/cookbook/loading_molecules.html"
+    "[Loading your data into Components]: https://docs.openfree.energy/en/stable/how_to_guides/loading_molecules.html"
    ]
   },
   {
@@ -167,7 +167,7 @@
    "source": [
     "To create an `AlchemicalNetwork` loop over the `LigandNetwork` edges and manually create the `Transformation` objects for each of them. This gives you full control over the entire network. For more information, see [Under the Hood]:\n",
     "\n",
-    "[Under the Hood]: https://docs.openfree.energy/en/stable/cookbook/under_the_hood.html"
+    "[Under the Hood]: https://docs.openfree.energy/en/stable/how_to_guides/under_the_hood.html"
    ]
   },
   {
@@ -282,9 +282,9 @@
     "tags": []
    },
    "source": [
-    "While the `AlchemicalNetwork` class itself has no on-disk representation, the `Transformation` instances that compose it do. Write an alchemical network to disk by iterating over its edges. For more information, see [Dumping a Transformation to JSON]:\n",
+    "While the `AlchemicalNetwork` class itself has no on-disk representation, the `Transformation` instances that compose it do. Write an alchemical network to disk by iterating over its edges. For more information, see [Writing a Transformation to JSON].\n",
     "\n",
-    "[Dumping a Transformation to JSON]: https://docs.openfree.energy/en/stable/cookbook/dumping_transformation.html"
+    "[Writing a Transformation to JSON]: https://docs.openfree.energy/en/stable/how_to_guides/dumping_transformation.html"
    ]
   },
   {
diff --git a/cookbook/generate_ligand_network.ipynb b/cookbook/generate_ligand_network.ipynb
index 3675c925..696dacec 100644
--- a/cookbook/generate_ligand_network.ipynb
+++ b/cookbook/generate_ligand_network.ipynb
@@ -29,9 +29,9 @@
    "id": "7f1a272a-ffe7-4397-a8a6-c590d3a210bc",
    "metadata": {},
    "source": [
-    "This cookbook assumes you have already loaded a collection of `SmallMoleculeComponent` objects into an iterable called `ligands`.\n",
+    "This How-to guide assumes you have already loaded a collection of `SmallMoleculeComponent` objects into an iterable called `ligands`.\n",
     "\n",
-    "For more information, see the [Loading Small Molecules Cookbook](https://docs.openfree.energy/en/stable/cookbook/loading_molecules.html#loading-small-molecules)."
+    "For more information, see the [Loading Small Molecules How-to guide](https://docs.openfree.energy/en/stable/how_to_guides/loading_molecules.html#loading-small-molecules)."
    ]
   },
   {
@@ -979,7 +979,7 @@
    "source": [
     "For more ways to visualize a `LigandNetwork`, see [Visualizing Ligand Networks].\n",
     "\n",
-    "[Visualizing Ligand Networks]: https://docs.openfree.energy/en/stable/cookbook/ligandnetwork_vis.html"
+    "[Visualizing Ligand Networks]: https://docs.openfree.energy/en/stable/how_to_guides/ligandnetwork_vis.html"
    ]
   },
   {
diff --git a/cookbook/hand_write_ligand_network.ipynb b/cookbook/hand_write_ligand_network.ipynb
index cd9891ab..18e8883c 100644
--- a/cookbook/hand_write_ligand_network.ipynb
+++ b/cookbook/hand_write_ligand_network.ipynb
@@ -21,8 +21,8 @@
     "\n",
     "Although this is the most flexible way to define a ``LigandNetwork``, we encourage you to use **openfe** helper functionality when possible for performance, reproducibility, and ease of use:\n",
     "\n",
-    "  - [Loading Ligand Networks Exported by Orion or FEP+](https://docs.openfree.energy/en/stable/cookbook/network_from_orion_fepp.html)\n",
-    "  - [Planning a Ligand Network](https://docs.openfree.energy/en/stable/cookbook/generate_ligand_network.html)\n"
+    "  - [Loading Ligand Networks Exported by Orion or FEP+](https://docs.openfree.energy/en/stable/how_to_guides/network_from_orion_fepp.html)\n",
+    "  - [Planning a Ligand Network](https://docs.openfree.energy/en/stable/how_to_guides/generate_ligand_network.html)\n"
    ]
   },
   {
@@ -38,9 +38,9 @@
    "id": "39e64f74-337e-4a88-b253-ab051820d5e3",
    "metadata": {},
    "source": [
-    "This cookbook assumes you've already loaded a collection of `SmallMoleculeComponent` objects into an iterable called `ligands`.\n",
+    "This How-to guide assumes you've already loaded a collection of `SmallMoleculeComponent` objects into an iterable called `ligands`.\n",
     "\n",
-    "For more information, see [Loading Small Molecules](https://docs.openfree.energy/en/stable/cookbook/loading_molecules.html#loading-small-molecules)."
+    "For more information, see [Loading Small Molecules](https://docs.openfree.energy/en/stable/how_to_guides/loading_molecules.html#loading-small-molecules)."
    ]
   },
   {
@@ -92,7 +92,7 @@
    "source": [
     "As we will only specify the topology of the network, OpenFE must generate atom mappings for us. For this, it needs an atom mapper; for more information, see [Choose an Atom Mapper]:\n",
     "\n",
-    "[Choose an Atom Mapper]: https://docs.openfree.energy/en/stable/cookbook/generate_ligand_network.html#Choose-an-atom-mapper"
+    "[Choose an Atom Mapper]: https://docs.openfree.energy/en/stable/how_to_guides/generate_ligand_network.html#Choose-an-atom-mapper"
    ]
   },
   {
@@ -240,7 +240,7 @@
    "source": [
     "For more ways to visualize a `LigandNetwork`, see [Visualizing Ligand Networks].\n",
     "\n",
-    "[Visualizing Ligand Networks]: https://docs.openfree.energy/en/stable/cookbook/ligandnetwork_vis.html"
+    "[Visualizing Ligand Networks]: https://docs.openfree.energy/en/stable/how_to_guides/ligandnetwork_vis.html"
    ]
   },
   {
diff --git a/cookbook/ligandnetwork_vis.ipynb b/cookbook/ligandnetwork_vis.ipynb
index 3e976950..79fb0ee2 100644
--- a/cookbook/ligandnetwork_vis.ipynb
+++ b/cookbook/ligandnetwork_vis.ipynb
@@ -39,7 +39,7 @@
    "id": "0d405db9-1ab5-43e1-aa51-89b5bdb283d7",
    "metadata": {},
    "source": [
-    "You will need to create a `LigandNetwork` for your system of interest. For more information, see [Generating a Ligand Network](https://docs.openfree.energy/en/stable/cookbook/generate_ligand_network.html)."
+    "You will need to create a `LigandNetwork` for your system of interest. For more information, see [Generating a Ligand Network](https://docs.openfree.energy/en/stable/how_to_guides/generate_ligand_network.html)."
    ]
   },
   {
diff --git a/cookbook/loading_molecules.ipynb b/cookbook/loading_molecules.ipynb
index e22783a9..74f4b5ef 100644
--- a/cookbook/loading_molecules.ipynb
+++ b/cookbook/loading_molecules.ipynb
@@ -246,7 +246,7 @@
    "source": [
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
-    "**Partial charges:** Any partial charges stored in an SDF file are read along with the molecules, and are used in simulations instead of generating new ones. The files used here already have AM1-BCC partial charges. To assign partial charges to your own molecules, see the cookbook on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/cookbook/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
+    "**Partial charges:** Any partial charges stored in an SDF file are read along with the molecules, and are used in simulations instead of generating new ones. The files used here already have AM1-BCC partial charges. To assign partial charges to your own molecules, see the How-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/chow_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
     "\n",
     "</div>"
    ]
diff --git a/cookbook/network_from_orion_fepp.ipynb b/cookbook/network_from_orion_fepp.ipynb
index 4dbaaa48..4d826500 100644
--- a/cookbook/network_from_orion_fepp.ipynb
+++ b/cookbook/network_from_orion_fepp.ipynb
@@ -35,7 +35,7 @@
    "source": [
     "Both FEP+ `.edge` and Orion `.dat` files identify molecules by name, so to load the network OpenFE requires a list of named ligands.\n",
     "\n",
-    "Load the ligands used by the network into instances of `SmallMoleculeComponent`. For more information, see [Loading Small Molecules](https://docs.openfree.energy/en/stable/cookbook/loading_molecules.html#loading-small-molecules)."
+    "Load the ligands used by the network into instances of `SmallMoleculeComponent`. For more information, see [Loading Small Molecules](https://docs.openfree.energy/en/stable/how_to_guides/loading_molecules.html#loading-small-molecules)."
    ]
   },
   {
@@ -87,7 +87,7 @@
    "source": [
     "Both formats encode only the network itself, leaving mappings between atoms in each edge undefined. OpenFE needs an atom mapper to produce atom mappings; for more information, see [Choose an Atom Mapper]:\n",
     "\n",
-    "[Choose an Atom Mapper]: https://docs.openfree.energy/en/stable/cookbook/generate_ligand_network.html#Choose-an-atom-mapper"
+    "[Choose an Atom Mapper]: https://docs.openfree.energy/en/stable/how_to_guides/generate_ligand_network.html#Choose-an-atom-mapper"
    ]
   },
   {
@@ -170,7 +170,7 @@
     "\n",
     "For more ways to visualize a `LigandNetwork`, see [Visualizing Ligand Networks].\n",
     "\n",
-    "[Visualizing Ligand Networks]: https://docs.openfree.energy/en/stable/cookbook/ligandnetwork_vis.html"
+    "[Visualizing Ligand Networks]: https://docs.openfree.energy/en/stable/how_to_guides/ligandnetwork_vis.html"
    ]
   },
   {
@@ -249,7 +249,7 @@
    "source": [
     "See [Creating an Alchemical Network] for how to use these defined `ligand_network` objects to create an AlchemicalNetwork, which can then be executed using the OpenFE CLI.\n",
     "\n",
-    "[Creating an Alchemical Network]: https://docs.openfree.energy/en/stable/cookbook/create_alchemical_network.html"
+    "[Creating an Alchemical Network]: https://docs.openfree.energy/en/stable/how_to_guides/create_alchemical_network.html"
    ]
   }
  ],
diff --git a/cookbook/repairing_broken_networks.ipynb b/cookbook/repairing_broken_networks.ipynb
index 4b4b67ed..59b6b4ca 100644
--- a/cookbook/repairing_broken_networks.ipynb
+++ b/cookbook/repairing_broken_networks.ipynb
@@ -10,7 +10,7 @@
     "In a relative binding free energy (RBFE) campaign, some `Transformations` may fail.\n",
     "If enough fail, the ligand network can become disconnected, and the ligands can no longer all be ranked against one another.\n",
     "\n",
-    "This cookbook follows the repair workflow end to end:\n",
+    "This How-to guide follows the repair workflow end to end:\n",
     "\n",
     "1. **Identify failures** from campaign results and reconstruct the broken network.\n",
     "2. **Repair the ligand network**, either manually or automatically by edge score.\n",
diff --git a/cookbook/rfe_alchemical_planners.ipynb b/cookbook/rfe_alchemical_planners.ipynb
index bbd015f2..b4ae865a 100644
--- a/cookbook/rfe_alchemical_planners.ipynb
+++ b/cookbook/rfe_alchemical_planners.ipynb
@@ -101,7 +101,7 @@
    "source": [
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
-    "**Partial charges:** The ligands in `somebenzenes_am1bcc.sdf` already have AM1-BCC partial charges, so the same charges are used in every repeat. To assign partial charges to your own ligands, see the cookbook on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/cookbook/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
+    "**Partial charges:** The ligands in `somebenzenes_am1bcc.sdf` already have AM1-BCC partial charges, so the same charges are used in every repeat. To assign partial charges to your own ligands, see the How-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
     "\n",
     "</div>"
    ]
diff --git a/cookbook/user_charges.ipynb b/cookbook/user_charges.ipynb
index b6bfc72d..f576514f 100644
--- a/cookbook/user_charges.ipynb
+++ b/cookbook/user_charges.ipynb
@@ -27,7 +27,7 @@
    "id": "717f695e-7841-4168-b820-87fe2eb29c72",
    "metadata": {},
    "source": [
-    "`SmallMoleculeComponent`s are usually loaded into OpenFE without partial charges, for example when loading from [SDF files](https://docs.openfree.energy/en/stable/cookbook/loading_molecules.html#Loading-small-molecules).\n",
+    "`SmallMoleculeComponent`s are usually loaded into OpenFE without partial charges, for example when loading from [SDF files](https://docs.openfree.energy/en/stable/how_to_guides/loading_molecules.html#Loading-small-molecules).\n",
     "\n",
     "In that case, partial charges are assigned by the `Protocol`, using the method defined in its `partial_charge_settings`. By default, this is AM1-BCC charges from AmberTools, using the input conformer.\n",
     "\n",
@@ -38,7 +38,7 @@
     "\n",
     "Both apply to the AM1-BCC-based methods. To avoid these issues, we recommend assigning partial charges once, before setting up any simulations, and storing them with your molecules. Any partial charges present on a `SmallMoleculeComponent` are used by the `Protocol` instead of generating new ones.\n",
     "\n",
-    "This cookbook shows how to do this with the Python API. To do the same from the command line, see the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html)."
+    "This How-to guide shows how to do this with the Python API. To do the same from the command line, see the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html)."
    ]
   },
   {
diff --git a/execution/task_based_execution_python_api.ipynb b/execution/task_based_execution_python_api.ipynb
index 132f7afc..5cf8d193 100644
--- a/execution/task_based_execution_python_api.ipynb
+++ b/execution/task_based_execution_python_api.ipynb
@@ -70,7 +70,7 @@
     "\n",
     "The input to a task-based campaign is an `AlchemicalNetwork`. If you don't\n",
     "have one yet, see the\n",
-    "[Create an `AlchemicalNetwork` cookbook](https://docs.openfree.energy/en/stable/cookbook/create_alchemical_network.html),\n",
+    "[Create an `AlchemicalNetwork` How-to guide](https://docs.openfree.energy/en/stable/how_to_guides/create_alchemical_network.html),\n",
     "or add `--networks-only` to an `openfe plan-rbfe-network` call.\n",
     "\n",
     "Here we use a small MCL-1 network with pre-charged ligands and two edges,\n",
@@ -1639,7 +1639,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.13.16"
+   "version": "3.13.14"
   }
  },
  "nbformat": 4,
diff --git a/openmm_md/plain_md.ipynb b/openmm_md/plain_md.ipynb
index a0c5996a..1f23ccfe 100644
--- a/openmm_md/plain_md.ipynb
+++ b/openmm_md/plain_md.ipynb
@@ -170,7 +170,7 @@
    "source": [
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
-    "**Partial charges:** The ligand in `benzene_am1bcc.sdf` already has AM1-BCC partial charges, so the same charges are used in every repeat. To assign partial charges to your own ligands, see the cookbook on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/cookbook/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
+    "**Partial charges:** The ligand in `benzene_am1bcc.sdf` already has AM1-BCC partial charges, so the same charges are used in every repeat. To assign partial charges to your own ligands, see the How-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
     "\n",
     "</div>"
    ]
diff --git a/openmm_septop/septop_tutorial.ipynb b/openmm_septop/septop_tutorial.ipynb
index ac94decf..12e8c43d 100644
--- a/openmm_septop/septop_tutorial.ipynb
+++ b/openmm_septop/septop_tutorial.ipynb
@@ -134,7 +134,7 @@
     "\n",
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
-    "**Learn more:** To assign partial charges to your own ligands, see the cookbook on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/cookbook/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
+    "**Learn more:** To assign partial charges to your own ligands, see the How-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
     "\n",
     "</div>"
    ]
diff --git a/rbfe_tutorial/rbfe_python_tutorial.ipynb b/rbfe_tutorial/rbfe_python_tutorial.ipynb
index 29d23f91..2b03c58b 100644
--- a/rbfe_tutorial/rbfe_python_tutorial.ipynb
+++ b/rbfe_tutorial/rbfe_python_tutorial.ipynb
@@ -62,7 +62,7 @@
     "\n",
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
-    "**Learn more:** To assign partial charges to your own ligands, see the cookbook on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/cookbook/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
+    "**Learn more:** To assign partial charges to your own ligands, see the How-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
     "\n",
     "</div>"
    ]
diff --git a/showcase/openfe_showcase.ipynb b/showcase/openfe_showcase.ipynb
index 6fe9a7eb..edd828b4 100644
--- a/showcase/openfe_showcase.ipynb
+++ b/showcase/openfe_showcase.ipynb
@@ -642,7 +642,7 @@
    "source": [
     "**2. `LomapAtomMapper`**\n",
     "\n",
-    "Alternatively, mappings can be generated using the MCS-based `LomapAtomMapper`. For more information on configuring and using this mapper, see the [ligand network generation cookbook](https://docs.openfree.energy/en/stable/cookbook/generate_ligand_network.html)."
+    "Alternatively, mappings can be generated using the MCS-based `LomapAtomMapper`. For more information on configuring and using this mapper, see the [ligand network generation How-to guide](https://docs.openfree.energy/en/stable/how_to_guides/generate_ligand_network.html)."
    ]
   },
   {
@@ -3281,7 +3281,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "\u001B[?25lLoading results:  ▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇  54/54 files\u001B[?25h\n",
+      "\u001b[?25lLoading results:  ▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇  54/54 files\u001b[?25h\n",
       "writing dg output to 'final_results.tsv'\n",
       "ligand\tDG(MLE) (kcal/mol)\tuncertainty (kcal/mol)\n",
       "lig_ejm_31\t-0.09\t0.06\n",
@@ -3412,20 +3412,12 @@
     "* [ABFE tutorial](https://docs.openfree.energy/en/latest/tutorials/abfe_tutorial.html)\n",
     "* [RBFE using a Separated Topologies (SepTop) approach tutorial](https://docs.openfree.energy/en/latest/tutorials/septop_tutorial.html)\n",
     "\n",
-    "In addition to the tutorials, you can find [cookbooks](https://docs.openfree.energy/en/latest/cookbook/index.html), written as How-to guides on how to utilize different components of the toolkit, as well as a [User Guide](https://docs.openfree.energy/en/latest/guide/index.html) that goes into the underlying concepts of the OpenFE toolkit.\n",
+    "In addition to the tutorials, you can find [How-to guides](https://docs.openfree.energy/en/latest/how_to_guides/index.html), written as How-to guides on how to utilize different components of the toolkit, as well as a [User Guide](https://docs.openfree.energy/en/latest/guide/index.html) that goes into the underlying concepts of the OpenFE toolkit.\n",
     "\n",
     "For details about the toolkit's core methods and classes, please visit our [API Reference](https://docs.openfree.energy/en/latest/reference/index.html) or our [Github page](https://github.com/OpenFreeEnergy/openfe).\n",
     "\n",
     "To learn more about the project, our team and how you can get involved, please visit our [Homepage](https://openfree.energy/) or get in touch at OpenFreeEnergy@omsf.io."
    ]
-  },
-  {
-   "metadata": {},
-   "cell_type": "code",
-   "outputs": [],
-   "execution_count": null,
-   "source": "",
-   "id": "eb2308d6adfdda77"
   }
  ],
  "metadata": {
@@ -3449,7 +3441,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.13.11"
+   "version": "3.13.14"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

From 731180eee08cc9c468accbadf530cbf16cf73b0c Mon Sep 17 00:00:00 2001
From: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
Date: Mon, 9 Nov 2026 09:48:10 +0100
Subject: [PATCH 02/11] Apply suggestion from @hannahbaumann

---
 abfe_tutorial/abfe_tutorial.ipynb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/abfe_tutorial/abfe_tutorial.ipynb b/abfe_tutorial/abfe_tutorial.ipynb
index d6f21af8..87a3aebf 100644
--- a/abfe_tutorial/abfe_tutorial.ipynb
+++ b/abfe_tutorial/abfe_tutorial.ipynb
@@ -130,7 +130,7 @@
     "\n",
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
-    "**Learn more:** To assign partial charges to your own ligands, see the How-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
+    "**Learn more:** To assign partial charges to your own ligands, see the how-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
     "\n",
     "</div>"
    ]

From b1da0b91244f8860149bab91d98a0c2d0147d95d Mon Sep 17 00:00:00 2001
From: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
Date: Mon, 9 Nov 2026 09:48:36 +0100
Subject: [PATCH 03/11] Apply suggestion from @hannahbaumann

---
 ahfe_tutorial/ahfe_tutorial.ipynb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ahfe_tutorial/ahfe_tutorial.ipynb b/ahfe_tutorial/ahfe_tutorial.ipynb
index bca79595..784b9891 100644
--- a/ahfe_tutorial/ahfe_tutorial.ipynb
+++ b/ahfe_tutorial/ahfe_tutorial.ipynb
@@ -122,7 +122,7 @@
    "source": [
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
-    "**Partial charges:** The ligand in `benzene_am1bcc.sdf` already has AM1-BCC partial charges, so the same charges are used in every repeat. To assign partial charges to your own ligands, see the How-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
+    "**Partial charges:** The ligand in `benzene_am1bcc.sdf` already has AM1-BCC partial charges, so the same charges are used in every repeat. To assign partial charges to your own ligands, see the how-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
     "\n",
     "</div>"
    ]

From d98742ad72726483720ecd9bc4d7d614197c2efe Mon Sep 17 00:00:00 2001
From: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
Date: Mon, 9 Nov 2026 09:49:00 +0100
Subject: [PATCH 04/11] Apply suggestion from @hannahbaumann

---
 cookbook/cofactors_rbfe.ipynb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cookbook/cofactors_rbfe.ipynb b/cookbook/cofactors_rbfe.ipynb
index 602a167b..380a49c3 100644
--- a/cookbook/cofactors_rbfe.ipynb
+++ b/cookbook/cofactors_rbfe.ipynb
@@ -7,7 +7,7 @@
    "source": [
     "# Defining Cofactors\n",
     "\n",
-    "This How-to guide demonstrates how to define cofactors (any small molecules that are not the bound ligand) with 1) the ``openfe`` CLI during the planning phase and 2) directly using the Python API.\n",
+    "This how-to guide demonstrates how to define cofactors (any small molecules that are not the bound ligand) with 1) the ``openfe`` CLI during the planning phase and 2) directly using the Python API.\n",
     "\n",
     "Similar to `ligand` definition, `cofactors` can be loaded from in SDF file format, and multiple molecules can be defined in a single file."
    ]

From b72166a2709901e8b0517935def5cc64f21b48ed Mon Sep 17 00:00:00 2001
From: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
Date: Mon, 9 Nov 2026 09:49:25 +0100
Subject: [PATCH 05/11] Apply suggestion from @hannahbaumann

---
 cookbook/create_alchemical_network.ipynb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cookbook/create_alchemical_network.ipynb b/cookbook/create_alchemical_network.ipynb
index a38d18a2..39792c93 100644
--- a/cookbook/create_alchemical_network.ipynb
+++ b/cookbook/create_alchemical_network.ipynb
@@ -51,7 +51,7 @@
    "id": "6bfee4c7-0aaf-49a6-b35a-bdbe99444bab",
    "metadata": {},
    "source": [
-    "This How-to guide assumes you've already loaded a `LigandNetwork`.\n",
+    "This how-to guide assumes you've already loaded a `LigandNetwork`.\n",
     "To learn how to build a `LigandNetwork`, see [Planning a Ligand Network](https://docs.openfree.energy/en/stable/how_to_guides/generate_ligand_network.html)."
    ]
   },

From c3ce13ab973a8af99178647f1552731ef058c913 Mon Sep 17 00:00:00 2001
From: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
Date: Mon, 9 Nov 2026 09:49:55 +0100
Subject: [PATCH 06/11] Apply suggestion from @hannahbaumann

---
 cookbook/create_alchemical_network.ipynb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cookbook/create_alchemical_network.ipynb b/cookbook/create_alchemical_network.ipynb
index 39792c93..06e0eb67 100644
--- a/cookbook/create_alchemical_network.ipynb
+++ b/cookbook/create_alchemical_network.ipynb
@@ -85,7 +85,7 @@
    "source": [
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
-    "**Partial charges:** The ligands in `somebenzenes_am1bcc.sdf` already have AM1-BCC partial charges, so the same charges are used in every repeat. To assign partial charges to your own ligands, see the How-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
+    "**Partial charges:** The ligands in `somebenzenes_am1bcc.sdf` already have AM1-BCC partial charges, so the same charges are used in every repeat. To assign partial charges to your own ligands, see the how-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
     "\n",
     "</div>"
    ]

From c4dc4baf5876dbf857453bf77ddcb2a548056d21 Mon Sep 17 00:00:00 2001
From: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
Date: Mon, 9 Nov 2026 09:50:22 +0100
Subject: [PATCH 07/11] Apply suggestion from @hannahbaumann

---
 cookbook/create_alchemical_network.ipynb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cookbook/create_alchemical_network.ipynb b/cookbook/create_alchemical_network.ipynb
index 06e0eb67..fe48c3c6 100644
--- a/cookbook/create_alchemical_network.ipynb
+++ b/cookbook/create_alchemical_network.ipynb
@@ -95,7 +95,7 @@
    "id": "405fe819-b4a6-408b-8623-041492c84dfb",
    "metadata": {},
    "source": [
-    "This How-to guide assumes you've already loaded a `Protocol`. For more information, see [Choose and Configure a Protocol]:\n",
+    "This how-to guide assumes you've already loaded a `Protocol`. For more information, see [Choose and Configure a Protocol]:\n",
     "\n",
     "[Choose and Configure a Protocol]: https://docs.openfree.energy/en/stable/how_to_guides/choose_protocol.html"
    ]

From 002e68accbcb3ee0a4b9ebd27b0b925cf279b2eb Mon Sep 17 00:00:00 2001
From: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
Date: Mon, 9 Nov 2026 09:50:47 +0100
Subject: [PATCH 08/11] Apply suggestion from @hannahbaumann

---
 cookbook/create_alchemical_network.ipynb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cookbook/create_alchemical_network.ipynb b/cookbook/create_alchemical_network.ipynb
index fe48c3c6..68279cd5 100644
--- a/cookbook/create_alchemical_network.ipynb
+++ b/cookbook/create_alchemical_network.ipynb
@@ -117,7 +117,7 @@
    "id": "0908d2b2-421d-4b51-8b35-d2cca5e25a95",
    "metadata": {},
    "source": [
-    "This How-to guide assumes you've already loaded a solvent and all the other chemical components of the system, including any proteins or cofactors. For more information, see [Loading your data into Components]:\n",
+    "This how-to guide assumes you've already loaded a solvent and all the other chemical components of the system, including any proteins or cofactors. For more information, see [Loading your data into Components]:\n",
     "\n",
     "[Loading your data into Components]: https://docs.openfree.energy/en/stable/how_to_guides/loading_molecules.html"
    ]

From 3300e8952d629bbd3c4fae11fc9e84fe6206dc00 Mon Sep 17 00:00:00 2001
From: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
Date: Mon, 9 Nov 2026 09:51:15 +0100
Subject: [PATCH 09/11] Apply suggestion from @hannahbaumann

---
 cookbook/generate_ligand_network.ipynb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cookbook/generate_ligand_network.ipynb b/cookbook/generate_ligand_network.ipynb
index 696dacec..b8c9f1c1 100644
--- a/cookbook/generate_ligand_network.ipynb
+++ b/cookbook/generate_ligand_network.ipynb
@@ -29,7 +29,7 @@
    "id": "7f1a272a-ffe7-4397-a8a6-c590d3a210bc",
    "metadata": {},
    "source": [
-    "This How-to guide assumes you have already loaded a collection of `SmallMoleculeComponent` objects into an iterable called `ligands`.\n",
+    "This how-to guide assumes you have already loaded a collection of `SmallMoleculeComponent` objects into an iterable called `ligands`.\n",
     "\n",
     "For more information, see the [Loading Small Molecules How-to guide](https://docs.openfree.energy/en/stable/how_to_guides/loading_molecules.html#loading-small-molecules)."
    ]

From 8873fc65cf8c487be760bc39f51c7bf6c6cf3d35 Mon Sep 17 00:00:00 2001
From: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
Date: Mon, 9 Nov 2026 09:51:54 +0100
Subject: [PATCH 10/11] Apply suggestion from @hannahbaumann

---
 cookbook/generate_ligand_network.ipynb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cookbook/generate_ligand_network.ipynb b/cookbook/generate_ligand_network.ipynb
index b8c9f1c1..85a3e3c9 100644
--- a/cookbook/generate_ligand_network.ipynb
+++ b/cookbook/generate_ligand_network.ipynb
@@ -31,7 +31,7 @@
    "source": [
     "This how-to guide assumes you have already loaded a collection of `SmallMoleculeComponent` objects into an iterable called `ligands`.\n",
     "\n",
-    "For more information, see the [Loading Small Molecules How-to guide](https://docs.openfree.energy/en/stable/how_to_guides/loading_molecules.html#loading-small-molecules)."
+    "For more information, see the [Loading Small Molecules how-to guide](https://docs.openfree.energy/en/stable/how_to_guides/loading_molecules.html#loading-small-molecules)."
    ]
   },
   {

From 2ef9841e9c9a637ad8a96756e7ed9b1783dddaa5 Mon Sep 17 00:00:00 2001
From: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
Date: Mon, 9 Nov 2026 09:55:39 +0100
Subject: [PATCH 11/11] Apply batched suggestions from code review

Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
---
 cookbook/hand_write_ligand_network.ipynb        | 2 +-
 cookbook/loading_molecules.ipynb                | 2 +-
 cookbook/repairing_broken_networks.ipynb        | 2 +-
 cookbook/rfe_alchemical_planners.ipynb          | 2 +-
 cookbook/user_charges.ipynb                     | 2 +-
 execution/task_based_execution_python_api.ipynb | 2 +-
 openmm_md/plain_md.ipynb                        | 2 +-
 openmm_septop/septop_tutorial.ipynb             | 2 +-
 rbfe_tutorial/rbfe_python_tutorial.ipynb        | 2 +-
 showcase/openfe_showcase.ipynb                  | 4 ++--
 10 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/cookbook/hand_write_ligand_network.ipynb b/cookbook/hand_write_ligand_network.ipynb
index 18e8883c..76c621dd 100644
--- a/cookbook/hand_write_ligand_network.ipynb
+++ b/cookbook/hand_write_ligand_network.ipynb
@@ -38,7 +38,7 @@
    "id": "39e64f74-337e-4a88-b253-ab051820d5e3",
    "metadata": {},
    "source": [
-    "This How-to guide assumes you've already loaded a collection of `SmallMoleculeComponent` objects into an iterable called `ligands`.\n",
+    "This how-to guide assumes you've already loaded a collection of `SmallMoleculeComponent` objects into an iterable called `ligands`.\n",
     "\n",
     "For more information, see [Loading Small Molecules](https://docs.openfree.energy/en/stable/how_to_guides/loading_molecules.html#loading-small-molecules)."
    ]
diff --git a/cookbook/loading_molecules.ipynb b/cookbook/loading_molecules.ipynb
index 74f4b5ef..cef65614 100644
--- a/cookbook/loading_molecules.ipynb
+++ b/cookbook/loading_molecules.ipynb
@@ -246,7 +246,7 @@
    "source": [
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
-    "**Partial charges:** Any partial charges stored in an SDF file are read along with the molecules, and are used in simulations instead of generating new ones. The files used here already have AM1-BCC partial charges. To assign partial charges to your own molecules, see the How-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/chow_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
+    "**Partial charges:** Any partial charges stored in an SDF file are read along with the molecules, and are used in simulations instead of generating new ones. The files used here already have AM1-BCC partial charges. To assign partial charges to your own molecules, see the how-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/chow_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
     "\n",
     "</div>"
    ]
diff --git a/cookbook/repairing_broken_networks.ipynb b/cookbook/repairing_broken_networks.ipynb
index 59b6b4ca..3aab32b4 100644
--- a/cookbook/repairing_broken_networks.ipynb
+++ b/cookbook/repairing_broken_networks.ipynb
@@ -10,7 +10,7 @@
     "In a relative binding free energy (RBFE) campaign, some `Transformations` may fail.\n",
     "If enough fail, the ligand network can become disconnected, and the ligands can no longer all be ranked against one another.\n",
     "\n",
-    "This How-to guide follows the repair workflow end to end:\n",
+    "This how-to guide follows the repair workflow end to end:\n",
     "\n",
     "1. **Identify failures** from campaign results and reconstruct the broken network.\n",
     "2. **Repair the ligand network**, either manually or automatically by edge score.\n",
diff --git a/cookbook/rfe_alchemical_planners.ipynb b/cookbook/rfe_alchemical_planners.ipynb
index b4ae865a..4e42f6f2 100644
--- a/cookbook/rfe_alchemical_planners.ipynb
+++ b/cookbook/rfe_alchemical_planners.ipynb
@@ -101,7 +101,7 @@
    "source": [
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
-    "**Partial charges:** The ligands in `somebenzenes_am1bcc.sdf` already have AM1-BCC partial charges, so the same charges are used in every repeat. To assign partial charges to your own ligands, see the How-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
+    "**Partial charges:** The ligands in `somebenzenes_am1bcc.sdf` already have AM1-BCC partial charges, so the same charges are used in every repeat. To assign partial charges to your own ligands, see the how-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
     "\n",
     "</div>"
    ]
diff --git a/cookbook/user_charges.ipynb b/cookbook/user_charges.ipynb
index f576514f..519aaba4 100644
--- a/cookbook/user_charges.ipynb
+++ b/cookbook/user_charges.ipynb
@@ -38,7 +38,7 @@
     "\n",
     "Both apply to the AM1-BCC-based methods. To avoid these issues, we recommend assigning partial charges once, before setting up any simulations, and storing them with your molecules. Any partial charges present on a `SmallMoleculeComponent` are used by the `Protocol` instead of generating new ones.\n",
     "\n",
-    "This How-to guide shows how to do this with the Python API. To do the same from the command line, see the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html)."
+    "This how-to guide shows how to do this with the Python API. To do the same from the command line, see the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html)."
    ]
   },
   {
diff --git a/execution/task_based_execution_python_api.ipynb b/execution/task_based_execution_python_api.ipynb
index 5cf8d193..3704c070 100644
--- a/execution/task_based_execution_python_api.ipynb
+++ b/execution/task_based_execution_python_api.ipynb
@@ -70,7 +70,7 @@
     "\n",
     "The input to a task-based campaign is an `AlchemicalNetwork`. If you don't\n",
     "have one yet, see the\n",
-    "[Create an `AlchemicalNetwork` How-to guide](https://docs.openfree.energy/en/stable/how_to_guides/create_alchemical_network.html),\n",
+    "[Create an `AlchemicalNetwork` how-to guide](https://docs.openfree.energy/en/stable/how_to_guides/create_alchemical_network.html),\n",
     "or add `--networks-only` to an `openfe plan-rbfe-network` call.\n",
     "\n",
     "Here we use a small MCL-1 network with pre-charged ligands and two edges,\n",
diff --git a/openmm_md/plain_md.ipynb b/openmm_md/plain_md.ipynb
index 1f23ccfe..f080ada8 100644
--- a/openmm_md/plain_md.ipynb
+++ b/openmm_md/plain_md.ipynb
@@ -170,7 +170,7 @@
    "source": [
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
-    "**Partial charges:** The ligand in `benzene_am1bcc.sdf` already has AM1-BCC partial charges, so the same charges are used in every repeat. To assign partial charges to your own ligands, see the How-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
+    "**Partial charges:** The ligand in `benzene_am1bcc.sdf` already has AM1-BCC partial charges, so the same charges are used in every repeat. To assign partial charges to your own ligands, see the how-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
     "\n",
     "</div>"
    ]
diff --git a/openmm_septop/septop_tutorial.ipynb b/openmm_septop/septop_tutorial.ipynb
index 12e8c43d..89b09373 100644
--- a/openmm_septop/septop_tutorial.ipynb
+++ b/openmm_septop/septop_tutorial.ipynb
@@ -134,7 +134,7 @@
     "\n",
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
-    "**Learn more:** To assign partial charges to your own ligands, see the How-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
+    "**Learn more:** To assign partial charges to your own ligands, see the how-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
     "\n",
     "</div>"
    ]
diff --git a/rbfe_tutorial/rbfe_python_tutorial.ipynb b/rbfe_tutorial/rbfe_python_tutorial.ipynb
index 2b03c58b..a0d74e95 100644
--- a/rbfe_tutorial/rbfe_python_tutorial.ipynb
+++ b/rbfe_tutorial/rbfe_python_tutorial.ipynb
@@ -62,7 +62,7 @@
     "\n",
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
-    "**Learn more:** To assign partial charges to your own ligands, see the How-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
+    "**Learn more:** To assign partial charges to your own ligands, see the how-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
     "\n",
     "</div>"
    ]
diff --git a/showcase/openfe_showcase.ipynb b/showcase/openfe_showcase.ipynb
index edd828b4..356593d2 100644
--- a/showcase/openfe_showcase.ipynb
+++ b/showcase/openfe_showcase.ipynb
@@ -642,7 +642,7 @@
    "source": [
     "**2. `LomapAtomMapper`**\n",
     "\n",
-    "Alternatively, mappings can be generated using the MCS-based `LomapAtomMapper`. For more information on configuring and using this mapper, see the [ligand network generation How-to guide](https://docs.openfree.energy/en/stable/how_to_guides/generate_ligand_network.html)."
+    "Alternatively, mappings can be generated using the MCS-based `LomapAtomMapper`. For more information on configuring and using this mapper, see the [ligand network generation how-to guide](https://docs.openfree.energy/en/stable/how_to_guides/generate_ligand_network.html)."
    ]
   },
   {
@@ -3412,7 +3412,7 @@
     "* [ABFE tutorial](https://docs.openfree.energy/en/latest/tutorials/abfe_tutorial.html)\n",
     "* [RBFE using a Separated Topologies (SepTop) approach tutorial](https://docs.openfree.energy/en/latest/tutorials/septop_tutorial.html)\n",
     "\n",
-    "In addition to the tutorials, you can find [How-to guides](https://docs.openfree.energy/en/latest/how_to_guides/index.html), written as How-to guides on how to utilize different components of the toolkit, as well as a [User Guide](https://docs.openfree.energy/en/latest/guide/index.html) that goes into the underlying concepts of the OpenFE toolkit.\n",
+    "In addition to the tutorials, you can find [how-to guides](https://docs.openfree.energy/en/latest/how_to_guides/index.html) on how to utilize different components of the toolkit, as well as a [User Guide](https://docs.openfree.energy/en/latest/guide/index.html) that goes into the underlying concepts of the OpenFE toolkit.\n",
     "\n",
     "For details about the toolkit's core methods and classes, please visit our [API Reference](https://docs.openfree.energy/en/latest/reference/index.html) or our [Github page](https://github.com/OpenFreeEnergy/openfe).\n",
     "\n",