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Structure-Based Approaches for Protein-Protein Interaction Prediction Using Machine Learning and Deep Learning

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Structure-Based Approaches for Protein-Protein Interaction Prediction Using Machine Learning and Deep Learning
Kiouri, Despoina P
Χασάπης, Χρήστος
Batsis, Georgios C
Άρθρο σε επιστημονικό περιοδικό
2025-01-17
Protein-Protein Interaction (PPI) prediction plays a pivotal role in understanding cellular processes and uncovering molecular mechanisms underlying health and disease. Structure-based PPI prediction has emerged as a robust alternative to sequence-based methods, offering greater biological accuracy by integrating three-dimensional spatial and biochemical features. This work summarizes the recent advances in computational approaches leveraging protein structure information for PPI prediction, focusing on machine learning (ML) and deep learning (DL) techniques. These methods not only improve predictive accuracy but also provide insights into functional sites, such as binding and catalytic residues. However, challenges such as limited high-resolution structural data and the need for effective negative sampling persist. Through the integration of experimental and computational tools, structure-based prediction paves the way for comprehensive proteomic network analysis, holding promise for advancements in drug discovery, biomarker identification, and personalized medicine. Future directions include enhancing scalability and dataset reliability to expand these approaches across diverse proteomes.
Δομική Βιολογία (EL)
Βιοχημεία (EL)
Βιοπληροφορική (EL)
Structural Biology (EN)
Biochemistry (EN)
Bioinformatics (EN)
computational biology (EL)
deep learning (EL)
structure representations (EL)
protein interaction mapping (EL)
proteomics (EL)
proteins (EL)
machine learning (EL)
humans (EL)
protein-protein interactions (EL)
English
Biomolecules
https://creativecommons.org/licenses/by/4.0/deed.el
: © 2025 by the authors. Licensee MDPI, Basel, Switzerland.
National Hellenic Research Foundation (NHRF)
Helios - Repository of the National Hellenic Research Foundation (NHRF)



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