diff --git a/wedock.ipynb b/wedock.ipynb
index 104df50..7f03d52 100644
--- a/wedock.ipynb
+++ b/wedock.ipynb
@@ -6,11 +6,39 @@
"id": "HlvKcskyTzu4"
},
"source": [
- "# **Basic Molecular Docking**\n",
+ "# **Programmatic Molecular Docking**\n",
"\n",
- "This **LABO****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 **LABODOCK****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": {