diff --git a/doc/FAQ.rst b/doc/FAQ.rst
index 83c9b713..16459b68 100644
--- a/doc/FAQ.rst
+++ b/doc/FAQ.rst
@@ -3,6 +3,6 @@ FAQ Notebooks
 
 .. toctree::
 
-   Missing_Contacts.ipynb
-   Comparing_CGs_Bars.ipynb
-   Comparing_CGs_Flares.ipynb
+   notebooks/Missing_Contacts.ipynb
+   notebooks/Comparing_CGs_Bars.ipynb
+   notebooks/Comparing_CGs_Flares.ipynb
diff --git a/doc/index.rst b/doc/index.rst
index 2deaf0d9..cbefa8b5 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -71,8 +71,9 @@ and calculates the  time-traces of residue-residue distances, and from there, **
 
    installation
    CLI Tutorial <overview>
-   API Jupyter Notebook Tutorial <Tutorial.ipynb>
-   Covid-19-Spike-Protein-Example.ipynb
+   API Jupyter Notebook Tutorial <notebooks/Tutorial.ipynb>
+   notebooks/Covid-19-Spike-Protein-Example.ipynb
+   notebooks/Covid-19-Spike-Protein-Interface.ipynb
    cli_cli/cli_cli
    api/api
    FAQ