PepFuNN

Purpose

Here we present PepFuNN, a package for the analysis of natural and modified peptides using a set of modules to study their sequences, including design of libraries, peptide clustering and similarity analysis.

Required third-party tools

The package depends on some external packages like RDKit (https://rdkit.org/) and BioPython (https://biopython.org/). Their licenses are included in the repository.

Quick installation

The project can be cloned to run a local pip installation pip install -e ..

The package can also be installed directly from Github with the following command:

pip install git+https://github.com/novonordisk-research/pepfunn.git

Main functions

Notebooks

A folder called notebooks include a set of jupyter scripts per module available in PepFuNN. The notebooks contain the main functionalities with various peptide sequences as input. The output files in the same folder to check and compare the obtained results.

Tests

A set of unit tests are available in the tests folder. These can be run separately per module by calling each test script, or all can be tested at the same time using the test.py file.

python test.py

References

If you use PepFuNN in your work, please cite the following papers:

• 'PepFuNN: Novo Nordisk open-source toolkit to enable peptide in silico analysis', Journal of Peptide Science, 2025. Link: https://onlinelibrary.wiley.com/doi/10.1002/psc.3666
• 'PepFun 2.0: improved protocols for the analysis of natural and modified peptides', Future Drug Discovery, 2023. Link: https://www.future-science.com/doi/10.4155/fdd-2023-0004
• 'PepFun: Open Source Protocols for Peptide-Related Computational Analysis', Molecules, 2021. Link: https://www.mdpi.com/1420-3049/26/6/1664

Contact

For any questions, please contact: raoc@novonordisk.com