Bhat, P.Patil, N.2026-02-052023Network Modeling Analysis in Health Informatics and Bioinformatics, 2023, Vol.12, 1, p. -21926662https://doi.org/10.1007/s13721-023-00427-0https://idr.nitk.ac.in/handle/123456789/28267The field of proteomics encompasses a comprehensive examination of proteins, encompassing their structural properties, interactions with other biomolecules, subcellular localization, functional roles, interaction sites, regions of disorder, and exploring novel protein designs. Each of these domains interlinks, contributing valuable information to the study of each other part. Extensive research in most of these areas has given rise to many more challenges that require further exploration. This review mainly concentrates on prediction approaches for protein–protein interaction sites, protein subcellular locations, and protein functions. We provide an exhaustive collection of several latest works in the above three domains, along with a digest of their descriptions in the most recent times. We conclude the review by highlighting the existing challenges and emphasizing the need for a deeper exploration of the research gaps in these studies. © 2023, The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.AccuracyF-scoreMatthews correlation coefficientPrecisionProtein functionProtein localizationProtein–protein interaction siteRecall