CycloPs_v2: A Cyclic Peptide Library Generator

CycloPs_v2 is a cyclic peptide library generator designed to facilitate the creation and exploration of diverse peptide libraries, including noncanonical and cyclic peptides. This package was released in its current state based on interest generated by the PeptideCLM model, as described in a bioRxiv paper.

Please cite the PeptideCLM paper (or its published version) if you use this package. A JOSS paper on CycloPs_v2 is forthcoming.

Usage Guide

1. Generate Peptides:

   • Run generate_randpeps.py to generate random peptide sequences.

2. Generate SMILES Notation:

   • Pass the resulting FASTA file to PepLibGen/StructGen/fasta.py for SMILES generation.
   • The output is a text file, with each line containing:

     {Comma-separated Amino Acids}-{cyclization notation}: {SMILES string}
     

3. Noncanonical Modifications:

   • The Jupyter notebook build_noncanon_aa.ipynb provides workflows for adding modifications like N-methylation and PEGylation.
   • These modifications will be packaged as functions in future releases.

4. Amino Acid Notation:

   • Notation for single-character amino acids is found in PepLibGen/StructGen/aminoacids.py.

Future Work

Improvements, including modular functions for peptide modifications and additional SMILES generation options, are in progress.

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CycloPs_v2 is a work in progress. Feedback and contributions are welcome as we continue to develop and refine this tool.