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diff --git a/.buildinfo b/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: c21fa86dd7455de717928e13edc055fc
+config: 27fd8099d12d965f77f9435b7060564e
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/_images/fig_1_kinomltechpaper_v2.png b/_images/fig_1_kinomltechpaper_v2.png
diff --git a/_images/notebooks_getting_started_24_0.png → _images/notebooks_getting_started_25_0.png b/_images/notebooks_getting_started_24_0.png → _images/notebooks_getting_started_25_0.png
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diff --git a/_images/notebooks_ligand-only-smiles-EGFR_56_23.png b/_images/notebooks_ligand-only-smiles-EGFR_56_23.png
diff --git a/_images/notebooks_ligand-only-smiles-EGFR_56_26.png b/_images/notebooks_ligand-only-smiles-EGFR_56_26.png
diff --git a/_images/notebooks_ligand-only-smiles-EGFR_56_29.png b/_images/notebooks_ligand-only-smiles-EGFR_56_29.png
diff --git a/_images/notebooks_ligand-only-smiles-EGFR_56_3.png b/_images/notebooks_ligand-only-smiles-EGFR_56_3.png
diff --git a/_images/notebooks_ligand-only-smiles-EGFR_56_6.png b/_images/notebooks_ligand-only-smiles-EGFR_56_6.png
diff --git a/_images/notebooks_ligand-only-smiles-EGFR_56_9.png b/_images/notebooks_ligand-only-smiles-EGFR_56_9.png
diff --git a/_sources/index.md.txt b/_sources/index.md.txt
@@ -10,30 +10,42 @@ If you are interested in this code, please wait for the official release to use
 
 ```
 
-# OpenKinome & KinoML
+# KinoML
 
-The [OpenKinome](https://openkinome.org) initiative aims to leverage the increasingly available bioactivity data and scalable computational resources to perform kinase-centric drug design in the context of structure-informed machine learning and free energy calculations. `KinoML` is the main library supporting these efforts.
+Welcome to the Documentation of KinoML! The documentation is divided into two parts:
+
+* **User guide**: in this section you will learn how to use KinoML to filter and download data from a data base, featurize your kinase data so that it is ML friendly and train and evaluate a ML model on your featurized kinase data. You will also learn about the KinoML object model, and how to access each of these objects. We also provide a detailed examples of how to use every featurizer implemented within KinoML.
+
+* **Experiment tutorials**: this section shows how to use KinoML to  ML structure-based experiments. All experiments are structure-based and they are all end to end, from data collection to model training and evaluation.
+
+
+
+KinoML falls under the [OpenKinome](https://openkinome.org) initiative, which aims to leverage the increasingly available bioactivity data and scalable computational resources to perform kinase-centric drug design in the context of structure-informed machine learning and free energy calculations. `KinoML` is the main library supporting these efforts.
 
 Do you want to know more about OpenKinome ecosystem? Check its [website](https://openkinome.org).
 
 <!-- Notify Sphinx about the TOC -->
 
 ```{toctree}
 :caption: User guide
-:maxdepth: 1
+:maxdepth: 3
 :hidden:
 
 notebooks/getting_started.nblink
 notebooks/kinoml_object_model.nblink
+notebooks/OpenEye_structural_featurizer.nblink
+notebooks/Schrodinger_structural_featurizer.nblink
 ```
 
 ```{toctree}
-:caption: Tutorials
-:maxdepth: 1
+:caption: Experiment tutorials
+:maxdepth: 2
 :hidden:
 
-notebooks/OpenEye_structural_featurizer.nblink
-notebooks/Schrodinger_structural_featurizer.nblink
+notebooks/ligand-only-smiles-EGFR.nblink
+notebooks/ligand-only-morgan1024-EGFR.nblink
+notebooks/kinase-ligand-informed-smiles-sequence-EGFR.nblink
+notebooks/kinase-ligand-informed-morgan-composition-EGFR.nblink
 ```
 
 ```{toctree}

diff --git a/_sources/notebooks/OpenEye_structural_featurizer.nblink.txt b/_sources/notebooks/OpenEye_structural_featurizer.nblink.txt
@@ -1 +1 @@
-{"path": "../../examples/OpenEye_structural_featurizer.ipynb"}
+{"path": "../../tutorials/getting_started/OpenEye_structural_featurizer_showcase.ipynb"}
diff --git a/_sources/notebooks/Schrodinger_structural_featurizer.nblink.txt b/_sources/notebooks/Schrodinger_structural_featurizer.nblink.txt
@@ -1 +1 @@
-{"path": "../../examples/Schrodinger_structural_featurizer.ipynb"}
+{"path": "../../tutorials/getting_started/Schrodinger_structural_featurizer_showcase.ipynb"}
diff --git a/_sources/notebooks/getting_started.nblink.txt b/_sources/notebooks/getting_started.nblink.txt
@@ -1 +1 @@
-{"path": "../../examples/getting_started.ipynb"}
+{"path": "../../tutorials/getting_started/getting_started_with_kinoml.ipynb"}
diff --git a/_sources/notebooks/kinase-ligand-informed-morgan-composition-EGFR.nblink.txt b/_sources/notebooks/kinase-ligand-informed-morgan-composition-EGFR.nblink.txt
@@ -0,0 +1 @@
+{"path": "../../tutorials/experiments/kinase-ligand-informed-morgan-composition-EGFR/experiments_notebook.ipynb"}
diff --git a/_sources/notebooks/kinase-ligand-informed-smiles-sequence-EGFR.nblink.txt b/_sources/notebooks/kinase-ligand-informed-smiles-sequence-EGFR.nblink.txt
@@ -0,0 +1 @@
+{"path": "../../tutorials/experiments/kinase-ligand-informed-smiles-sequence-EGFR/experiment_notebook.ipynb"}
diff --git a/_sources/notebooks/kinoml_object_model.nblink.txt b/_sources/notebooks/kinoml_object_model.nblink.txt
@@ -1 +1 @@
-{"path": "../../examples/kinoml_object_model.ipynb", "extra-media": ["../../kinoml/data/"]}
+{"path": "../../tutorials/getting_started/kinoml_object_model.ipynb", "extra-media": ["../../kinoml/data/"]}
diff --git a/_sources/notebooks/ligand-only-morgan1024-EGFR.nblink.txt b/_sources/notebooks/ligand-only-morgan1024-EGFR.nblink.txt
@@ -0,0 +1 @@
+{"path": "../../tutorials/experiments/ligand-only-morgan1024-EGFR/experiment_notebook.ipynb"}
diff --git a/_sources/notebooks/ligand-only-smiles-EGFR.nblink.txt b/_sources/notebooks/ligand-only-smiles-EGFR.nblink.txt
@@ -0,0 +1 @@
+{"path": "../../tutorials/experiments/ligand-only-smiles-EGFR/experiment_notebook.ipynb"}
diff --git a/api/kinoml/_version/index.html b/api/kinoml/_version/index.html
@@ -55,8 +55,8 @@
     <link rel="stylesheet" type="text/css" href="../../../_static/twemoji.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/graphviz.css" />
-    <link rel="stylesheet" type="text/css" href="../../../_static/panels-bootstrap.5fd3999ee7762ccc51105388f4a9d115.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/panels-main.c949a650a448cc0ae9fd3441c0e17fb0.css" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/panels-bootstrap.5fd3999ee7762ccc51105388f4a9d115.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/panels-variables.06eb56fa6e07937060861dad626602ad.css" />
     <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
     <script src="../../../_static/jquery.js"></script>
@@ -226,7 +226,7 @@
     <li class="md-nav__item">
 
 
-      <a href="../../../notebooks/getting_started.html" class="md-nav__link">Getting Started</a>
+      <a href="../../../notebooks/getting_started.html" class="md-nav__link">Getting started with KinoML</a>
 
 
     </li>
@@ -239,20 +239,48 @@
     </li>
     <li class="md-nav__item">
 
-      <span class="md-nav__link caption"><span class="caption-text">Tutorials</span></span>
+
+      <a href="../../../notebooks/OpenEye_structural_featurizer.html" class="md-nav__link">OpenEye Structural Featurizer</a>
+
 
     </li>
     <li class="md-nav__item">
 
 
-      <a href="../../../notebooks/OpenEye_structural_featurizer.html" class="md-nav__link">OpenEye Structural Featurizer</a>
+      <a href="../../../notebooks/Schrodinger_structural_featurizer.html" class="md-nav__link">Schrodinger Structural Featurizer</a>
 
 
     </li>
     <li class="md-nav__item">
 
+      <span class="md-nav__link caption"><span class="caption-text">Experiment tutorials</span></span>
 
-      <a href="../../../notebooks/Schrodinger_structural_featurizer.html" class="md-nav__link">Schrodinger Structural Featurizer</a>
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="../../../notebooks/ligand-only-smiles-EGFR.html" class="md-nav__link">Ligand-only SMILES experiment</a>
+
+
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="../../../notebooks/ligand-only-morgan1024-EGFR.html" class="md-nav__link">Ligand-only morgan 1024 experiment</a>
+
+
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="../../../notebooks/kinase-ligand-informed-smiles-sequence-EGFR.html" class="md-nav__link">Kinase informed SMILES experiment</a>
+
+
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="../../../notebooks/kinase-ligand-informed-morgan-composition-EGFR.html" class="md-nav__link">Kinase informed morgan 1024 experiment</a>
 
 
     </li>
@@ -277,7 +305,39 @@
 
 
       <a href="../index.html#submodules" class="md-nav__link">Submodules</a>
+      <ul class="md-nav__list"> 
+    <li class="md-nav__item">
+
+
+    <input class="md-toggle md-nav__toggle" data-md-toggle="toc" type="checkbox" id="__toc">
+    <label class="md-nav__link md-nav__link--active" for="__toc"> <code class="xref py py-mod docutils literal notranslate"><span class="pre">kinoml._version</span></code> </label>
+
+      <a href="#" class="md-nav__link md-nav__link--active"><code class="xref py py-mod docutils literal notranslate"><span class="pre">kinoml._version</span></code></a>
 
+
+<nav class="md-nav md-nav--secondary">
+    <label class="md-nav__title" for="__toc">"Contents"</label>
+  <ul class="md-nav__list" data-md-scrollfix="">
+        <li class="md-nav__item"><a href="#api-kinoml-version-index--page-root" class="md-nav__link"><code class="xref py py-mod docutils literal notranslate"><span class="pre">kinoml._version</span></code></a><nav class="md-nav">
+              <ul class="md-nav__list">
+        <li class="md-nav__item"><a href="#module-contents" class="md-nav__link">Module Contents</a>
+        </li></ul>
+            </nav>
+        </li>
+
+
+  </ul>
+</nav>
+
+
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="../utils/index.html" class="md-nav__link"><code class="xref py py-mod docutils literal notranslate"><span class="pre">kinoml.utils</span></code></a>
+
+
+    </li></ul>
 
     </li>
     <li class="md-nav__item">

diff --git a/api/kinoml/analysis/index.html b/api/kinoml/analysis/index.html
@@ -55,8 +55,8 @@
     <link rel="stylesheet" type="text/css" href="../../../_static/twemoji.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/graphviz.css" />
-    <link rel="stylesheet" type="text/css" href="../../../_static/panels-bootstrap.5fd3999ee7762ccc51105388f4a9d115.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/panels-main.c949a650a448cc0ae9fd3441c0e17fb0.css" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/panels-bootstrap.5fd3999ee7762ccc51105388f4a9d115.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/panels-variables.06eb56fa6e07937060861dad626602ad.css" />
     <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
     <script src="../../../_static/jquery.js"></script>
@@ -226,7 +226,7 @@
     <li class="md-nav__item">
 
 
-      <a href="../../../notebooks/getting_started.html" class="md-nav__link">Getting Started</a>
+      <a href="../../../notebooks/getting_started.html" class="md-nav__link">Getting started with KinoML</a>
 
 
     </li>
@@ -239,20 +239,48 @@
     </li>
     <li class="md-nav__item">
 
-      <span class="md-nav__link caption"><span class="caption-text">Tutorials</span></span>
+
+      <a href="../../../notebooks/OpenEye_structural_featurizer.html" class="md-nav__link">OpenEye Structural Featurizer</a>
+
 
     </li>
     <li class="md-nav__item">
 
 
-      <a href="../../../notebooks/OpenEye_structural_featurizer.html" class="md-nav__link">OpenEye Structural Featurizer</a>
+      <a href="../../../notebooks/Schrodinger_structural_featurizer.html" class="md-nav__link">Schrodinger Structural Featurizer</a>
 
 
     </li>
     <li class="md-nav__item">
 
+      <span class="md-nav__link caption"><span class="caption-text">Experiment tutorials</span></span>
 
-      <a href="../../../notebooks/Schrodinger_structural_featurizer.html" class="md-nav__link">Schrodinger Structural Featurizer</a>
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="../../../notebooks/ligand-only-smiles-EGFR.html" class="md-nav__link">Ligand-only SMILES experiment</a>
+
+
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="../../../notebooks/ligand-only-morgan1024-EGFR.html" class="md-nav__link">Ligand-only morgan 1024 experiment</a>
+
+
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="../../../notebooks/kinase-ligand-informed-smiles-sequence-EGFR.html" class="md-nav__link">Kinase informed SMILES experiment</a>
+
+
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="../../../notebooks/kinase-ligand-informed-morgan-composition-EGFR.html" class="md-nav__link">Kinase informed morgan 1024 experiment</a>
 
 
     </li>
@@ -270,8 +298,96 @@
 
 
       <a href="../index.html#subpackages" class="md-nav__link">Subpackages</a>
+      <ul class="md-nav__list"> 
+    <li class="md-nav__item">
+
+
+    <input class="md-toggle md-nav__toggle" data-md-toggle="toc" type="checkbox" id="__toc">
+    <label class="md-nav__link md-nav__link--active" for="__toc"> <code class="xref py py-mod docutils literal notranslate"><span class="pre">kinoml.analysis</span></code> </label>
+
+      <a href="#" class="md-nav__link md-nav__link--active"><code class="xref py py-mod docutils literal notranslate"><span class="pre">kinoml.analysis</span></code></a>
+
+
+<nav class="md-nav md-nav--secondary">
+    <label class="md-nav__title" for="__toc">"Contents"</label>
+  <ul class="md-nav__list" data-md-scrollfix="">
+        <li class="md-nav__item"><a href="#api-kinoml-analysis-index--page-root" class="md-nav__link"><code class="xref py py-mod docutils literal notranslate"><span class="pre">kinoml.analysis</span></code></a><nav class="md-nav">
+              <ul class="md-nav__list">
+        <li class="md-nav__item"><a href="#submodules" class="md-nav__link">Submodules</a>
+        </li></ul>
+            </nav>
+        </li>
+
+
+  </ul>
+</nav>
+
+
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="../core/index.html" class="md-nav__link"><code class="xref py py-mod docutils literal notranslate"><span class="pre">kinoml.core</span></code></a>
+
+
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="../databases/index.html" class="md-nav__link"><code class="xref py py-mod docutils literal notranslate"><span class="pre">kinoml.databases</span></code></a>
+
+
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="../datasets/index.html" class="md-nav__link"><code class="xref py py-mod docutils literal notranslate"><span class="pre">kinoml.datasets</span></code></a>
+
+
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="../docking/index.html" class="md-nav__link"><code class="xref py py-mod docutils literal notranslate"><span class="pre">kinoml.docking</span></code></a>
+
+
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="../features/index.html" class="md-nav__link"><code class="xref py py-mod docutils literal notranslate"><span class="pre">kinoml.features</span></code></a>
 
 
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="../ml/index.html" class="md-nav__link"><code class="xref py py-mod docutils literal notranslate"><span class="pre">kinoml.ml</span></code></a>
+
+
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="../modeling/index.html" class="md-nav__link"><code class="xref py py-mod docutils literal notranslate"><span class="pre">kinoml.modeling</span></code></a>
+
+
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="../optimize/index.html" class="md-nav__link"><code class="xref py py-mod docutils literal notranslate"><span class="pre">kinoml.optimize</span></code></a>
+
+
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="../workflows/index.html" class="md-nav__link"><code class="xref py py-mod docutils literal notranslate"><span class="pre">kinoml.workflows</span></code></a>
+
+
+    </li></ul>
+
     </li>
     <li class="md-nav__item">
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		{"path": "../../examples/OpenEye_structural_featurizer.ipynb"}
		{"path": "../../tutorials/getting_started/OpenEye_structural_featurizer_showcase.ipynb"}
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		{"path": "../../examples/Schrodinger_structural_featurizer.ipynb"}
		{"path": "../../tutorials/getting_started/Schrodinger_structural_featurizer_showcase.ipynb"}
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		@@ -1 +1 @@
		{"path": "../../examples/getting_started.ipynb"}
		{"path": "../../tutorials/getting_started/getting_started_with_kinoml.ipynb"}
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		@@ -0,0 +1 @@
		{"path": "../../tutorials/experiments/kinase-ligand-informed-morgan-composition-EGFR/experiments_notebook.ipynb"}
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		@@ -1 +1 @@
		{"path": "../../examples/kinoml_object_model.ipynb", "extra-media": ["../../kinoml/data/"]}
		{"path": "../../tutorials/getting_started/kinoml_object_model.ipynb", "extra-media": ["../../kinoml/data/"]}
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		@@ -0,0 +1 @@
		{"path": "../../tutorials/experiments/ligand-only-morgan1024-EGFR/experiment_notebook.ipynb"}