Εξειδίκευση τύπου :	Άρθρο σε επιστημονικό περιοδικό
Τίτλος:	Structure-Based Deep Learning Framework for Modeling Human-Gut Bacterial Protein Interactions
Δημιουργός/Συγγραφέας:	Kiouri, Despoina P Batsis, Georgios C [EL] Χασάπης, Χρήστος[EN] Chasapis, Christos
Ημερομηνία:	2025-02-17
Γλώσσα:	Αγγλικά
ISSN:	2227-7382
DOI:	10.3390/proteomes13010010
Άλλο:	39982320
Περίληψη:	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.
Τίτλος πηγής δημοσίευσης:	Proteomes
Τόμος/Κεφάλαιο:	13
Τεύχος:	1
Θεματική Κατηγορία:	[EL] Βιοπληροφορική[EN] Bioinformatics [EL] Δομική Βιολογία[EN] Structural Biology [EL] Μικροβιολογία[EN] Microbiology [EL] Βιοχημεία[EN] Biochemistry
Λέξεις-Κλειδιά:	deep learning gut microbiome host–bacteria interactions neural networks
Κάτοχος πνευματικών δικαιωμάτων:	© 2025 by the authors. Licensee MDPI, Basel, Switzerland.
Όροι και προϋποθέσεις δικαιωμάτων:	This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/ licenses/by/4.0/).
Ηλεκτρονική διεύθυνση στον εκδότη (link):	https://doi.org/10.3390/proteomes13010010
Σημειώσεις:	This article is a Technical Note.
Εμφανίζεται στις συλλογές:	Ινστιτούτο Χημικής Βιολογίας - Επιστημονικό έργο