diff --git a/models/rfd3/docs/tutorials/enzyme_design_tutorial.md b/models/rfd3/docs/tutorials/enzyme_design_tutorial.md
index 19d674d..01b5207 100644
--- a/models/rfd3/docs/tutorials/enzyme_design_tutorial.md
+++ b/models/rfd3/docs/tutorials/enzyme_design_tutorial.md
@@ -174,4 +174,4 @@ You have now set up an RFD3 calculation and successfully ran the inference code
 ## References and Further Reading
 - For more information on the different inference settings in RFD3, see {doc}`../input`
 - The calculation presented here was used to benchmark RFdiffusion2, for more information see [Atom-level enzyme active site scaffolding using RFdiffusion2](https://www.nature.com/articles/s41592-025-02975-x)
-- A more thorough discussion of the settings and configuration options in RFD3 can be found [here](../intro_inference_calculations.md)
\ No newline at end of file
+- A more thorough discussion of the settings and configuration options in RFD3 can be found {doc}`here <../intro_inference_calculations>`
\ No newline at end of file
diff --git a/models/rfd3/docs/tutorials/na_binder_tutorial.md b/models/rfd3/docs/tutorials/na_binder_tutorial.md
index 4d30904..2288bcb 100644
--- a/models/rfd3/docs/tutorials/na_binder_tutorial.md
+++ b/models/rfd3/docs/tutorials/na_binder_tutorial.md
@@ -211,5 +211,5 @@ For your actual projects, you would want to filter the designed structures based
 
 (na-references-and-further-reading)=
 ## References and Further Reading
-- For more information on the different inference settings in RFD3, see [input.md](../input.md)
-- A more thorough discussion of the settings and configuration options in RFD3 can be found [here](../intro_inference_calculations.md)
\ No newline at end of file
+- For more information on the different inference settings in RFD3, see {doc}`input.md <../input>`
+- A more thorough discussion of the settings and configuration options in RFD3 can be found {doc}`here <../intro_inference_calculations>`
\ No newline at end of file
diff --git a/models/rfd3/docs/tutorials/ppi_design_tutorial.md b/models/rfd3/docs/tutorials/ppi_design_tutorial.md
index 3e80be8..9335ef9 100644
--- a/models/rfd3/docs/tutorials/ppi_design_tutorial.md
+++ b/models/rfd3/docs/tutorials/ppi_design_tutorial.md
@@ -154,9 +154,9 @@ Feel free to go through the [other tutorials](https://rosettacommons.github.io/f
 
 (ppi-references-and-further-reading)=
 ## References and Further Reading
-- For more information on the different inference settings in RFD3, see [input.md](input.md)
+- For more information on the different inference settings in RFD3, see {doc}`input.md <../input>`
 - For more information on the example used here, see [*De novo design of protein structure and function with RFdiffusion*](https://www.nature.com/articles/s41586-023-06415-8#Sec12) by Joeseph L. Watson, et. al.
-- A more thorough discussion of the settings and configuration options in RFD3 can be found [here](intro_inference_calculations.md)
+- A more thorough discussion of the settings and configuration options in RFD3 can be found {doc}`here <../intro_inference_calculations>`