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v1.2.1
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@RyanZR
RyanZR committed Oct 9, 2023
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45 changes: 30 additions & 15 deletions CHANGELOG.md
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# Change Log
All notable changes to this repository will be documented in this file.

## [1.2.1] - 2023-08-12
### Added
+ [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MAJOR Added `--cpu` parameter in %vina
+ [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) MAJOR Added `--cpu` parameter in %vina

### Changed
+ [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MAJOR Upgraded packages: py3Dmol 2.0.3, rdkit-pypi 2022.9.5, biopython 1.80, openbabel 3.1.1, zlib 1.2.13
+ [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MINOR Renamed LABOGRID to [LaBOX](https://github.com/RyanZR/LaBOX)
+ [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) MAJOR Upgraded packages: py3Dmol 2.0.3, rdkit-pypi 2022.9.5, biopython 1.80, openbabel 3.1.1, zlib 1.2.13
+ [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) MINOR Renamed LABOGRID to [LaBOX](https://github.com/RyanZR/LaBOX)

### Fixed
+ [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MAJOR Fixed incomplete visualisation of protein-ligand interactions in `VIEW_PILE()`
+ [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) MAJOR Fixed incomplete visualisation of protein-ligand interactions in `VIEW_PILE()`

## [1.2.0] - 2023-02-12
### Added
+ [basic_molecular_docking.ipynb](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MAJOR Added 5 methods for defining grid box
+ [basic_molecular_docking.ipynb](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MINOR Added `showHs` argument in `VIEW_LIG()`
+ [virtual_screening.ipynb](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) MAJOR Added 5 methods for defining grid box
+ [virtual_screening.ipynb](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) MINOR Added `showHs` argument in `VIEW_LIG()`
+ [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MAJOR Added 5 methods for defining grid box
+ [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MINOR Added `showHs` argument in `VIEW_LIG()`
+ [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) MAJOR Added 5 methods for defining grid box
+ [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) MINOR Added `showHs` argument in `VIEW_LIG()`

### Changed
+ [basic_molecular_docking.ipynb](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MINOR Removed `showBestPose` argument in `VIEW_PILE()`
+ [basic_molecular_docking.ipynb](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MINOR Removed `AllChem.MMFFOptimizeMolecule()` in `VIEW_LIG()`
+ [virtual_screening.ipynb](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) MINOR Removed `AllChem.MMFFOptimizeMolecule()` in `VIEW_LIG()`
+ [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MINOR Removed `showBestPose` argument in `VIEW_PILE()`
+ [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MINOR Removed `AllChem.MMFFOptimizeMolecule()` in `VIEW_LIG()`
+ [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) MINOR Removed `AllChem.MMFFOptimizeMolecule()` in `VIEW_LIG()`

### Fixed
+ [basic_molecular_docking.ipynb](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MINOR Fixed spelling mistake in "Display 3D binding mode" section
+ [virtual_screening.ipynb](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) MINOR Fixed spelling mistake in "Display 3D binding mode" section
+ [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MINOR Fixed spelling mistake in "*Display 3D binding mode*" section
+ [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) MINOR Fixed spelling mistake in "*Display 3D binding mode*" section

## [1.0.0] - 2023-02-08
### Added
+ [basic_molecular_docking.ipynb](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MAJOR Added into 📁 notebooks.
+ [virtual_screening.ipynb](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) MAJOR Added into 📁 notebooks.
+ [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MAJOR Added into 📁 notebooks.
+ [virtual_screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb) MAJOR Added into 📁 notebooks.

### Changed
+ [🍊MOUNTAIN_V2.ipynb](https://github.com/RyanZR/labodock/blob/main/deprecated/%F0%9F%8D%8AMOUNTAIN_V2.ipynb) MAJOR No longer support and preceded by [basic_molecular_docking.ipynb](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb).
+ [🍊UNION_V2.ipynb](https://github.com/RyanZR/labodock/blob/main/deprecated/%F0%9F%8D%8AUNION_V2.ipynb) MAJOR No longer support and preceded by [virtual_screening.ipynb](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb).
+ [🍊PLIA_V2.ipynb](https://github.com/RyanZR/labodock/blob/main/deprecated/%F0%9F%8D%8APLIA_V2.ipynb) MAJOR No longer support but integrated into respective notebooks
+ [🍊MOUNTAIN_V2](https://github.com/RyanZR/labodock/blob/main/deprecated/%F0%9F%8D%8AMOUNTAIN_V2.ipynb) MAJOR No longer support and superseded by [basic_molecular_docking.ipynb](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb).
+ [🍊UNION_V2](https://github.com/RyanZR/labodock/blob/main/deprecated/%F0%9F%8D%8AUNION_V2.ipynb) MAJOR No longer support and superseded by [virtual_screening.ipynb](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb).
+ [🍊PLIA_V2](https://github.com/RyanZR/labodock/blob/main/deprecated/%F0%9F%8D%8APLIA_V2.ipynb) MAJOR No longer support but integrated into respective notebooks

### Fixed
+ [basic_molecular_docking.ipynb](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MINOR Fixed bug in `VIEW_PILE()`.
+ [basic_molecular_docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb) MINOR Fixed bug in `VIEW_PILE()`.
12 changes: 7 additions & 5 deletions README.md
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![LABODOCK](https://github.com/RyanZR/labodock/blob/main/res/labodock_banner.jpg)

# Effortless Docking with Google Colab
[![status](https://img.shields.io/badge/status-stable-success)](https://github.com/RyanZR/labodock)
[![version](https://img.shields.io/badge/version-1.2.0-blue)](https://github.com/RyanZR/labodock/tree/main/notebooks)
> UPDATE: Fixed packages installation issues. MAJOR UPDATE in code base coming soon with better readability and optimisation. Stay tunned!
[![status](https://img.shields.io/badge/status-pass-green)](https://github.com/RyanZR/labodock)
[![version](https://img.shields.io/badge/version-1.2.1-blue)](https://github.com/RyanZR/labodock/tree/main/notebooks)
[![size](https://img.shields.io/github/repo-size/RyanZR/labodock)](https://github.com/RyanZR/labodock)
[![license](https://img.shields.io/badge/license-MIT-informational)](https://github.com/RyanZR/labodock/blob/main/LICENSE)


**LABODOCK** is a repository where you can find a collection of Jupyter Notebooks for conducting structure-based molecular docking protocols interactively using Autodock Vina and PLIP on Google Colab. The main goal is to demonstrate the power of cloud-computing for conducting docking operations in an effortless and automated manner.

+ [Basic Molecular docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb)
+ [Basic Molecular Docking](https://github.com/RyanZR/labodock/blob/main/notebooks/basic_molecular_docking.ipynb)
+ [Virtual Screening](https://github.com/RyanZR/labodock/blob/main/notebooks/virtual_screening.ipynb)

**Important:** Do not use the `Run all` option. Run the `Install dependencies and softwares` cell individually and wait for the session to restart. **After that**, you can run all cells if you want. Thank you for your support.


## Features
+ Automated molecular docking operation
+ intuitive and interactive user interface
+ Five grid box defining methods: [LABOGRID](https://github.com/RyanZR/labogrid), [eBoxSize](https://github.com/michal-brylinski/eboxsize) ...
+ Intuitive and interactive user interface
+ Five grid box defining methods: [LaBOX](https://github.com/RyanZR/LaBOX), [eBoxSize](https://github.com/michal-brylinski/eboxsize) ...
+ Autodock Vina and Protein-Ligand Interaction Profiler integration
+ 3D Docking result and docking socres clustering

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