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.

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.

Renewable Energy Sources provide a viable solution to the problem of ever-increasing climate change. For this reason, several countries focus on electricity production using alternative sources. In this paper, the optimal positioning of the installation of wave energy converters is examined taking into account geospatial and technical limitations. Geospatial constraints depend on Land Use classes and seagrass of the coastal areas, while technical limitations include meteorological conditions and the morphology of the seabed. Suitable installation areas are selected after the exclusion of points that do not meet the aforementioned restrictions. We implemented a Deep Neural Network that operates based on heterogeneous data fusion, in this case satellite images and time series of meteorological data. This fact implies the definition of a two-branches architecture. The branch that is trained with image data provides for the localization of dynamic geospatial classes in the potential installation area, whereas the second one is responsible for the classification of the region according to the potential wave energy using wave height and period time series. In making the final decision on the suitability of the potential area, a large number of static land use data play an important role. These data are combined with neural network predictions for the optimizing positioning of the Wave Energy Converters. For the sake of completeness and flexibility, a Multi-Task Neural Network is developed. This model, in addition to predicting the suitability of an area depending on seagrass patterns and wave energy, also predicts land use classes through Multi-Label classification process. The proposed methodology is applied in the marine area of the city of Sines, Portugal. The first neural network achieves 98.7% Binary Classification accuracy, while the Multi-Task Neural Network 97.5% in the same metric and 93.5% in the F1 score of the Multi-Label classification output.

The gut microbiome, a complex ecosystem of microorganisms, plays a pivotal role in human health and disease. The gut microbiome’s influence extends beyond the digestive system to various organs, and its imbalance is linked to a wide range of diseases, including cancer and neurodevelopmental, inflammatory, metabolic, cardiovascular, autoimmune, and psychiatric diseases. Despite its significance, the interactions between gut bacteria and human proteins remain understudied, with less than 20,000 experimentally validated protein interactions between the host and any bacteria species. This study addresses this knowledge gap by predicting a protein–protein interaction network between gut bacterial and human proteins. Using statistical associations between Pfam domains, a comprehensive dataset of over one million experimentally validated pan-bacterial–human protein interactions, as well as inter- and intra-species protein interactions from various organisms, were used for the development of a machine learning-based prediction method to uncover key regulatory molecules in this dynamic system. This study’s findings contribute to the understanding of the intricate gut microbiome–host relationship and pave the way for future experimental validation and therapeutic strategies targeting the gut microbiome interplay.