Cited by 4Bioinformatics and Genomic NetworksMachine Learning in BioinformaticsComputational Drug Discovery Methods

Structure-Based Deep Learning Framework for Modeling Human–Gut Bacterial Protein Interactions

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Kiouri, Despoina P., Batsis, Georgios C., Chasapis, Christos T.·2025·Proteomes

Abstract

Background: The interaction network between the human host proteins and the proteins of the gut bacteria is essential for the establishment of human health, and its dysregulation directly contributes to disease development. Despite its great importance, experimental data on protein–protein interactions (PPIs) between these species are sparse due to experimental limitations. Methods: This study presents a deep learning-based framework for predicting PPIs between human and gut bacterial proteins using structural data. The framework leverages graph-based protein representations and variational autoencoders (VAEs) to extract structural embeddings from protein graphs, which are then fused through a Bi-directional Cross-Attention module to predict interactions. The model addresses common challenges in PPI datasets, such as class imbalance, using focal loss to emphasize harder-to-classify samples. Results: The results demonstrated that this framework exhibits robust performance, with high precision and recall across validation and test datasets, underscoring its generalizability. By incorporating proteoforms in the analysis, the model accounts for the structural complexity within proteomes, making predictions biologically relevant. Conclusions: These findings offer a scalable tool for investigating the interactions between the host and the gut microbiota, potentially yielding new treatment targets and diagnostics for disorders linked to the microbiome.

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  • Host-microbe interaction modeling using systems biology, metabolic network reconstruction, and in silico simulations provides insight into potential functional impacts and strain-specific mechanisms, supporting hypothesis generation before clinical validation.

    “Host–microbe interaction modeling, using systems biology, metabolic network reconstruction, and in silico simulations, provides insight into potential functional impacts and strain-specific mechanisms, supporting hypothesis generation before clinical validation [158].”

    From Current Concepts in Probiotic Safety and Efficacy (2026) · cites this paper as [158]

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  1. [42]Wu L. Tian Y. Huang Y. Li S. Lin H. Chawla N.V. Li S.Z. Mape-ppi: Towards effective and efficient protein-protein interaction prediction via microenvironment-aware protein embedding arXiv 2024 2402.14391

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Authors
Kiouri, D. P., Batsis, G. C., & Chasapis, C. T.
Affiliations
  • National and Kapodistrian University of Athens (GR)
  • National Hellenic Research Foundation (GR)
Corresponding author
Chasapis, Christos T.
Venue
Proteomes
Publisher
MDPI AG
Published
2025-02-17
Volume
13
Issue
1
Pages
10
ISSN
2227-7382 (ISSN-L)
OpenAlex
W4407642374
Cited by
3
References
68
Citations by year
2026: 1 · 2025: 2
FWCI
0.90
Type
journal article
Language
en
Open access
Locations
  • Proteomes (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • National Hellenic Research Foundation Helios Repository (National Hellenic Research Foundation) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
National Research Foundation
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
  • Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
Keywords
protein-protein interaction prediction, protein structure, variational autoencoder, cross-attention fusion, class imbalance, focal loss, proteoforms, gut microbiota

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