Add files via upload

wedock.ipynb

@@ -6,11 +6,39 @@
     "id": "HlvKcskyTzu4"
    },
    "source": [
-    "# **Basic Molecular Docking**\n",
+    "# **Programmatic Molecular Docking**\n",
     "\n",
-    "This <font color='orange'>**LABO**</font>**DOCK** notebook is designed for conducting basic molecular docking procedures using **Autodock Vina 1.2.5** and performing binding interaction analysis with **PLIP 2.3.0**. \n",
+    "This <font color='orange'>**LABODOCK**</font>**BINDER** notebook is designed for conducting basic molecular docking procedures using **Autodock Vina 1.2.5** and performing binding interaction analysis with **PLIP 2.3.0**. \n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Introduction\n",
+    "labodock_binder is an enhanced iteration of Labodock (https://github.com/RyanZR/labodock), with a primary focus on improved accessibility and user-friendliness. Notable modifications from Labodock version 2.0.0 include:\n",
+    "\n",
+    "**Seamless Access**: Unlike the original Google Colab login requirement, labodock_binder allows free access from Chrome, Firefox, and Safari, without the need for signup or login. This is made possible through the implementation of Binder technology (https://mybinder.org/).\n",
     "\n",
-    "- Please replace the next 3 string value, then from top left **Run** click ***Run All Cells**\n"
+    "**Pre-built Images**: The labodock_binder image is pre-built. When a user clicks the link, the image is pulled from the cloud to the local browser, instead of installing all packages from scratch. This significantly accelerates the readiness for docking.\n",
+    "\n",
+    "**Simplified Execution**: labodock_binder streamlines the process with one-click execution, eliminating the need for repetitive variable modifications.\n",
+    "\n",
+    "These enhancements collectively contribute to a more user-friendly and accessible experience. labodock_binder emerges as a versatile and convenient tool for users worldwide, requiring only internet availability—no Google account necessary.\n",
+    "\n",
+    "## Usage\n",
+    "**PDB_ID** is a four-letter code from the PDB bank website, for example, 3HTB\n",
+    "\n",
+    "**Native_lig** below means the native ligand of the co-crystal structure of the PDB bank, it can be found on the PDB website, it should always be a three-letter code, for example, JZ4\n",
+    "\n",
+    "**smiles** is the small molecule you want to dock, you can obtain this from ChemDraw, from **Edit** > **Copy as smiles**"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Please replace the next 3 string value, then from top left **Run** click ***Run All Cells**"
    ]
   },
   {
@@ -2871,6 +2899,23 @@
     "\n",
     "show_cscale({Show_protein: Protein_style}, {Show_surface: Surface_style})"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# References:\n",
+    "\n",
+    "- AutoDock Vina 1.2.5 (https://vina.scripps.edu/)\n",
+    "- Meeko 0.5.0 (https://github.com/forlilab/Meeko)\n",
+    "- OpenBabel 3.1.1 (https://github.com/openbabel/openbabel)\n",
+    "- PLIP 2.3.0 (https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index)\n",
+    "- Py3Dmol 2.0.3 (https://pypi.org/project/py3Dmol/)\n",
+    "- Rdkit 2023.9.1 (https://github.com/rdkit/rdkit)\n",
+    "- Spyrmsd 0.6.0 (https://github.com/RMeli/spyrmsd)\n",
+    "\n",
+    "- This browser docking experience wouldn't be possible without using Binder (https://mybinder.org/)"
+   ]
   }
  ],
  "metadata": {