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MULoc-target: Targeting peptide classification and detection using a protein language model.

Yuexu Jiang^1,2, Duolin Wang², Shuai Zeng²

¹Department of Chemical and Materials Engineering, University of Kentucky, 177, 512 Administration Dr F. Paul Anderson Tower, Lexington, KY 40506, United States.

Briefings in Bioinformatics

|August 27, 2025

Summary

This study presents MULoc-Target, a new deep-learning tool for identifying and classifying protein targeting peptides in eukaryotes. It achieves high accuracy and reveals important motif patterns for understanding protein sorting.

Keywords:

deep learning parameter efficient fine tuning peptide classification and detection protein language model protein localization protein targeting peptide

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Area of Science:

Molecular Biology
Bioinformatics
Computational Biology

Background:

Protein targeting directs proteins to specific cellular locations, crucial for cell function.
Accurate identification of targeting peptides is essential for understanding protein sorting mechanisms.
Existing methods may lack comprehensive capabilities for diverse targeting peptide detection.

Purpose of the Study:

Introduce MULoc-Target, a novel deep-learning method for detecting and classifying eukaryotic protein targeting peptides.
Develop and validate MULoc-Target using a curated benchmark dataset of eight targeting peptide types.
Provide insights into targeting peptide properties and mechanisms through motif pattern extraction.

Main Methods:

Developed MULoc-Target, a deep-learning model for protein targeting peptide analysis.
Curated a benchmark dataset with manually annotated eukaryotic targeting peptides.
Evaluated performance on benchmark and external datasets, comparing against existing methods.

Main Results:

MULoc-Target demonstrated state-of-the-art or competitive performance in detecting and classifying targeting peptides.
The method successfully extracted enriched motif patterns from targeting peptides.
Identified motifs showed strong alignment with known biological features of targeting peptides.

Conclusions:

MULoc-Target is a powerful and accurate tool for eukaryotic protein targeting peptide analysis.
The extracted motifs offer valuable insights into the functional properties of targeting peptides.
A publicly accessible web server and inference code are provided for broader use.