Code near final, update environment

README.md

@@ -1,2 +1,14 @@
-# iqb-2024
-Notebooks and environment set up for IQB 2024 workshop
+# Python Scripting for Molecular Docking
+
+## PDB Crash Course 2024
+
+Authors: Jessica A. Nash and Paul A. Craig
+
+Four notebooks and an environment have been set up for the IQB 2024 workshop, (Python Scripting for Molecular Docking)[https://iqb.rutgers.edu/node/284] to be held on Thursday, July 18., 2024.
+
+## Notebooks
+
+1. Enzyme Commission Class with Ligands (EC_ligand_search.ipynb)
+2. Visualizing the Binding Site of a Protein-Ligand Complex (binding_site_investigation.ipynb)
+3. Modifying Ligands with RDKit(molecule_manipulation.ipynb)
+4. Docking with AutoDock Vina (docking_single_ligand.ipynb)

binding_site_investigation.ipynb

@@ -337,7 +337,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "! pdb2pqr --pdb-output=structures/protein_h.pdb --pH=7.4 structures/protein_2zq2.pdb protein.pqr"
+    "! pdb2pqr --pdb-output=structures/protein_h.pdb --pH=7.4 structures/protein_2zq2.pdb structures/protein_2zq2.pqr"
    ]
   },
   {
@@ -533,6 +533,14 @@
    "source": [
     "fp.plot_3d(lig_list[0], protein_mol, frame=0)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "97ef5c4e-f5f5-43ce-9cd7-c0fc30e61538",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {