CyclicPepedia: A knowledge base of natural and synthetic cyclic peptides

Lei Liu^{1, #}, Liu Yang^{2, #}, Suqi Cao², Zhigang Gao³, Bin Yang⁴, Guoqing Zhang^{5, *}, Ruixin Zhu^{1, *}, Dingfeng Wu^{2, *}

Web crawling

The /Web crawling directory stores the crawler codes of different data source.

Environment

Build a Docker image through dockerfile or pull docker image through this link:docker pull registry.cn-hangzhou.aliyuncs.com/dfwlab/cyclicpepedia:20240106. You can use this image with the following command like: docker run -it -p 80:8888 -v $(PWD):/Cyclicpepedia $imageName:$tag /bin/bash. And then install the Jupyterlab by pip install jupyterlab and lanch it by jupyter lab --allow-root --ip=0.0.0.0 --port=8888.

Dataset

The /Dataset directory stores the main data resources of the CyclicPepedia, and you can also download these data from the Downloads of CyclicPepedia.

Tools

Codes in /Tools for the cyclic peptide tool used by CyclicPepedia and its test notebooks. You need to ensure that the program is valid in the same environment (build a Docker image through dockerfile and pip install jupyterlab), or pull docker image through this link:docker pull registry.cn-hangzhou.aliyuncs.com/dfwlab/cyclicpepedia:20240106.

• Struc2Seq (structure2sequence.py) and Test_Struc2seq.ipynb
• Seq2Struc (sequence2structure.py) and Test_Seq2struc.ipynb
• ga (graph_alignment.py) and Test_GraphAlignment.ipynb
• pp (peptide_properties.py) and Test_Peptide_properties.ipynb
• RDKit_format_issue.ipynb