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CyclicPepedia: A knowledge base of natural and synthetic cyclic peptides

Lei Liu1, #, Liu Yang2, #, Suqi Cao2, Zhigang Gao3, Bin Yang4, Guoqing Zhang5, *, Ruixin Zhu1, *, Dingfeng Wu2, *

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

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