# MDDeep-Ace: species-specific acetylation site prediction based on multi-domain adaptation

**Authors:** Yu Liu, Chaofan Ye, Can Lin, Kangkang Mao, Ming Zhu

PMC · DOI: 10.7717/peerj.19649 · 2025-07-03

## TL;DR

MDDeep-Ace is a new deep learning tool that improves prediction of acetylation sites in proteins across different species.

## Contribution

MDDeep-Ace introduces a multi-domain adaptation approach to enhance species-specific acetylation site prediction.

## Key findings

- MDDeep-Ace improves prediction accuracy across multiple species.
- The multi-domain adaptation approach outperforms existing lysine acetylation site prediction tools.

## Abstract

Lysine post-translational modification (PTM) is pivotal in regulating diverse cellular processes, profoundly impacting protein structure and function. Over recent decades, numerous experimental techniques have advanced PTM site identification, significantly contributing to research progress. However, these methods are time-intensive and labor-intensive. Deep learning technologies have shown promise in predicting PTM sites, yet current approaches struggle with species-specific PTM site prediction.

We introduce MDDeep-Ace, a novel deep learning method based on multi-domain adaptation for predicting lysine acetylation sites. By integrating data from multiple species, MDDeep-Ace enhances the generalization of species-specific prediction models, improving predictive performance.

Experimental findings illustrate that our proposed multi-domain adaptation approach significantly enhances prediction accuracy across multiple species, surpassing existing lysine acetylation site prediction tools.

## Full-text entities

- **Genes:** ADRB2 (adrenoceptor beta 2) [NCBI Gene 154] {aka ADRB2R, ADRBR, ARB2, B2AR, BAR, BETA2AR}
- **Diseases:** PTM (OMIM:614922), asthma (MESH:D001249)
- **Chemicals:** serine (MESH:D012694), S (MESH:D013455), chlorophyll (MESH:D002734), Glycine (MESH:D005998), Lysine (MESH:D008239), K (MESH:D011188)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], Rattus norvegicus (brown rat, species) [taxon 10116], S. japonicum [taxon 349478], Saccharomyces cerevisiae (baker's yeast, species) [taxon 4932], Plasmodium falciparum (malaria parasite P. falciparum, species) [taxon 5833], Homo sapiens (human, species) [taxon 9606], Arabidopsis thaliana (mouse-ear cress, species) [taxon 3702], Escherichia coli (E. coli, species) [taxon 562]

## Figures

25 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12229145/full.md

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Source: https://tomesphere.com/paper/PMC12229145