Review comments

Author: IAlibay

cookbook/openfold3_to_openfe.ipynb

@@ -51,9 +51,11 @@
     "\n",
     "2. Processing the OpenFold3 output for use with OpenFE\n",
     "\n",
-    "  * a) Choosing a reference protein structure\n",
-    "  * b) Aligning & extracting the ncessary ligands & protein structures.\n",
-    "  * c) Fixing & protonating the reference protein structure.\n",
+    "    a) Choosing a reference protein structure\n",
+    "\n",
+    "    b) Aligning & extracting the necessary ligands & protein structures.\n",
+    "\n",
+    "    c) Fixing & protonating the reference protein structure.\n",
     "\n",
     "\n",
     "3. Loading structures into OpenFE Components\n",
@@ -142,6 +144,16 @@
     "We then create the JSON file that will be the OpenFold input."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "b3f0be0c-144c-4e96-9310-a8778111291c",
+   "metadata": {},
+   "source": [
+    "<div class=\"alert alert-block alert-info\"> \n",
+    "  <b>Note:</b> In this example, we did not use the full FASTA sequence from UNIPROT for TYK2, but rather the sequence of the crystallographic structure.\n",
+    "</div>"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 3,