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labodock_binder

Open-sourced docking for small molecule to protein target. It prioritizes enhanced user-friendliness and accessibility.

https://github.com/quantaosun/labodock_binder

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (4.5%) to scientific vocabulary

Keywords

docking medicinal-chemistry protein-ligand
Last synced: 6 months ago · JSON representation ·

Repository

Open-sourced docking for small molecule to protein target. It prioritizes enhanced user-friendliness and accessibility.

Basic Info
  • Host: GitHub
  • Owner: quantaosun
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: main
  • Homepage:
  • Size: 1.47 MB
Statistics
  • Stars: 5
  • Watchers: 1
  • Forks: 3
  • Open Issues: 0
  • Releases: 6
Topics
docking medicinal-chemistry protein-ligand
Created about 2 years ago · Last pushed 10 months ago
Metadata Files
Readme License Citation

README.md

Labodock_binder

MySkills

The most reliable manner is to install this reposititory to a local Linux/Mac with conda based on environment.yml provided. But if you do not have a Linux and/or Conda environment, you can still use the cloud version below.

Cloud

badge

The RCSB server sometime is not working properly, in that case, you can manually download the native ligand SDF file and upload to the cloud.

image

In-house receptor docking

Binder

Use on Windows

My Skills

Install Docker-desktop, and start it on the back. Launched Windows PowerShell (The blue one) and have navigate to a folder where you want to do docking. Run:

docker pull qutesun/labodock_binder docker run -p 8888:8888 -v ${PWD}:/home/jovyan/work qutesun/labodock_binder Your PowerShell terminal will output some crazy lines that you probably can't read properly, among which there will be a token pin, just copy it.

Now go to your default browser, and try

localhost:8888 your browser will start a Jupyter Notebook interface and ask for a token pin, which you have coped from the backend in the PowerShell interface.

After having entered the browser interface, double click wedock_win.ipynb, and you are ready to do the docking just as if you using the Binder badge above.

DOI

version

license

百度

登陆百度飞浆，在公开项目中搜索本仓库名称，复刻到本人名下，点击启动环境运行，在命令行内生成新环境后，开始在笔记本内完成对接。受制于百度平台的维护策略，在项目关闭后我们创建的环境将被清除，下次启动时请再次安装。

image

Deploy on digitalOcean

This is strongly recomanded if you want to access the docking service 24/7

image

Create an droplet with the docker image as indicated above, open the firewall for port 8888, run the two lines of code to start the docking service

``` docker pull qutesun/labodock_binder

docker run -p 8888:8888 -v "$(pwd)":/home/jovyan/work -e NBUID=$(id -u) -e NBGID=$(id -g) qutesun/labodock_binder start-notebook.sh --NotebookApp.ip='0.0.0.0' --NotebookApp.port=8888 --NotebookApp.token='batman'

`` Assume your ip address of DigitalOcean instance is178.xxx.xxxx.xxx, you should be able to acess the docking jupyter notebook via your browser viahttp://178.xxx.xxxx.xxx:8888/lab, then input the passwordbatman` as defined in the docker run command (you can change it)

----------------------------Updated on April 2025 --------------------------------------

Acknowledgments

  • Credits to the Labodock project for developing an excellent and open-source suite for docking on Google Colab.
  • Credits to the Binder project for developing the fantastic interactive Jupiter notebook used on web browsers.

Owner

  • Name: Sun
  • Login: quantaosun
  • Kind: user
  • Location: China

Medicinal Chemistry/Modelling

Citation (CITATION.cff) 

cff-version: 0.0.2
message: "If you use this software, please cite it as below."
authors:
- family-names: "Sun"
  given-names: "Quantao"
orcid: https://orcid.org/0009-0004-7537-2703
title: "labodock_binder_v_0.0.2"
version: 0.0.2
doi: 10.5281/zenodo.10208365
date-released: 2023-11-24
repository-code: https://github.com/quantaosun/labodock_binder
keywords:
  - "drug design"
  - "molecular docking"
  - "virtual screening"
  - "web browser"
  - "autodock vina"
license: MIT
url: "https://github.com/quantaosun/labodock_binder"

GitHub Events

Total
  • Issues event: 1
  • Watch event: 2
  • Issue comment event: 2
  • Push event: 5
  • Fork event: 1
Last Year
  • Issues event: 1
  • Watch event: 2
  • Issue comment event: 2
  • Push event: 5
  • Fork event: 1

Dependencies

environment.yml pypi
  • meeko ==0.5.0
  • rdkit ==2023.9.1