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": {