antpack 0.1.5.2

A Python package for processing, manipulating and making inferences about antibody sequence data

AntPack

AntPack is a toolkit for data processing, statistical inference and machine learning for antibody sequences. It is currently in active development -- more updates soon! For installation and how to use, see the docs.

Antibody numbering

Numbering antibody sequences is an important precursor for many statistical inference / machine learning applications. AntPack is orders of magnitude faster for numbering antibody sequences than existing tools in the literature (e.g. ANARCI, AbRSA), while providing >= reliability.

Humanness and developability

Minimizing the risk of immunogenicity is important for selecting clinical candidates. In AntPack v0.1.0, we introduce a simple, fully interpretable generative model for human heavy and light chains that outperforms all comparators in the literature on a large held-out test set for distinguishing human sequences from those of other species. This scoring tool can be used to score sequences for humanness, suggest modifications to make them more human, identify liabilities, and generate highly human sequences that contain selected motifs.

Citing this work

If using AntPack in research intended for publication, please cite:

Jonathan Parkinson and Wei Wang. 2024. For antibody sequence generative modeling, mixture models may be all you need. bioRxiv: https://doi.org/10.1101/2024.01.27.577555