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.
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.
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 ${PWD}:/home/jovyan/work qutesun/labodock_binder
Your PowerShell terminal will output some crazy lines that you probably can't read properly, among which there will be a token pin, just copy it.
Now go to your default browser, and try
localhost:8888
your browser will start a Jupyter Notebook interface and ask for a token pin, which you have coped from the backend in the PowerShell interface.
After having entered the browser interface, double click wedock_win.ipynb, and you are ready to do the docking just as if you using the Binder badge above.
登陆百度飞浆，在公开项目中搜索本仓库名称，复刻到本人名下，点击启动环境运行，在命令行内生成新环境后，开始在笔记本内完成对接。受制于百度平台的维护策略，在项目关闭后我们创建的环境将被清除，下次启动时请再次安装。
This is strongly recomanded if you want to access the docking service 24/7
Create an droplet with the docker image as indicated above, open the firewall for port 8888, run the two lines of code to start the docking service
docker pull qutesun/labodock_binder
docker run -p 8888:8888 -v "$(pwd)":/home/jovyan/work -e NB_UID=$(id -u) -e NB_GID=$(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 is 178.xxx.xxxx.xxx, you should be able to acess the docking jupyter notebook via your browser via http://178.xxx.xxxx.xxx:8888/lab, then input the password batman as defined in the docker run command (you can change it)
----------------------------Updated on April 2025 --------------------------------------