# mimicDetector: a pipeline for protein motif mimicry detection in host-pathogen interactions

## TL;DR

This paper introduces a new tool called mimicDetector that helps find protein motifs in pathogens that mimic host proteins, which could help explain how pathogens evade the immune system.

## Contribution

The novel contribution is a k-mer-based pipeline for detecting protein motif mimicry in host-pathogen interactions with improved sensitivity and specificity.

## Key findings

- mimicDetector identified biologically plausible mimicry candidates in 17 important pathogens.
- Examples include helminth proteins mimicking human complement system components and a Leishmania infantum mimic of Reticulon-4.
- The pipeline is freely available and compatible with Unix-based systems.

## Abstract

Molecular mimicry is used by pathogens to evade the host immune system and manipulate other host cellular processes. It is often mediated by short motifs in non-homologous proteins, whose detection challenges the sensitivity and specificity of existing bioinformatics tools.

We present mimicDetector, a k-mer-based pipeline for identifying protein-level molecular mimicry between pathogens and their hosts. Applied to 17 globally important pathogens, mimicDetector identified a broad and biologically plausible set of mimicry candidates, including helminth proteins mimicking components of the human complement system and a Leishmania infantum mimic of Reticulon-4, a regulator of immune cell recruitment.

mimicDetector is freely available at https://github.com/kayleerich/mimicDetector/, implemented in Python and Snakemake, and compatible with Unix-based systems.