what's next

app.py

@@ -256,6 +256,7 @@ def plot_protein(result_df) -> str:
     
     return pdb_file
 
+
 # Function to plot a CIF file
 def show_cif_file(cif_file):
     """Plot a 3D structure from a CIF file with the Molecule3D library.
@@ -278,6 +279,7 @@ def show_cif_file(cif_file):
     
     return str(pdb_file)
 
+
 # Create the Gradio interface
 reps = [{"model": 0,"style": "cartoon","color": "hydrophobicity"}]
 
@@ -343,6 +345,16 @@ with gr.Blocks(theme=theme) as demo:
             label="MCP demonstration video"
         )
         
+        gr.Markdown(
+        """
+        # MCP tools
+        1. `create_fasta_file`: Create a FASTA file from a protein sequence string with a unique name.
+        2. `create_json_config`: Create a JSON configuration file from the Gradio interface inputs.
+        3. `compute_Chai1`: Compute a Chai-1 simulation on Modal labs server. Return a DataFrame with protein scores.
+        4. `plot_protein`: Plot the 3D structure of a protein using the DataFrame from `compute_Chai1` (Use for Gradio interface).
+        5. `show_cif_file`: Plot a 3D structure from a CIF file with the Molecule3D library (Use for the Gradio interface).
+        """)
+        
         with open("introduction_page.md", "r") as f:
             intro_md = f.read()
         gr.Markdown(intro_md)
@@ -358,6 +370,12 @@ with gr.Blocks(theme=theme) as demo:
     
         gr.Markdown(
         """
+        # What's next?
+        1. Expose additional tools to post-process the results of the simulations. 
+        The current post-processong tools are suited for the Gradio interface (ex: Plot images of the molecule structure from a file).
+        2. Continue the pipeline by adding softawres like [OpenMM](https://openmm.org/) or [Gromacs](https://www.gromacs.org/) for molecular dynamics simulations.
+        3. Perform complete simulation plans including loops over parameters fully automated by the LLM.
+        
         # Contact
         For any issues or questions, please contact the developer or refer to the documentation.
         """)