Structure-Based Deep Learning Framework for Modeling Human–Gut Bacterial Protein Interactions
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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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Current Concepts in Probiotic Safety and Efficacy
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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 [158].”
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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)
- PMC
- PMC11843979
- OpenAlex
- W4407642374
- Cited by
- 3
- References
- 68
- Citations by year
- 2026: 1 · 2025: 2
- FWCI
- 0.90
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- 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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