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Protein-Protein Interactions (PPIs) are fundamental in various biological processes and play a key role in life activities. The growing demand and cost of experimental PPI assays require computational methods for efficient PPI prediction.…
Polyphenols and proteins are essential biomolecules that influence food functionality and, by extension, human health. Their interactions -- hereafter referred to as PhPIs (polyphenol-protein interactions) -- affect key processes such as…
Here we present Translocatome, the first dedicated database of human translocating proteins. The core of the Translocatome database is the manually curated data set of 213 human translocating proteins listing the source of their…
Deep learning-based computational methods have achieved promising results in predicting protein-protein interactions (PPIs). However, existing benchmarks predominantly focus on isolated pairwise evaluations, overlooking a model's capability…
Aberrant protein-protein interactions (PPIs) underpin a plethora of human diseases, and disruption of these harmful interactions constitute a compelling treatment avenue. Advances in computational approaches to PPI prediction have closely…
Protein-protein interaction (PPI) prediction is an important problem in machine learning and computational biology. However, there is no data set for training or evaluation purposes, where all the instances are accurately labeled. Instead,…
Breast cancer is the most common cancer in women worldwide, and discovering the biomarkers of this disease became so vital nowadays and Cell in Cell structure could be one of them, and it may be used as an available proxy for tumor…
A mutation in a protein-coding gene in DNA can alter the protein structure coded by the same gene. Structurally altered proteins usually lose their functions and sometimes gain an undesirable function instead. These types of mutations and…
Accurate prediction of virus-host interactions is critical for understanding viral ecology and developing applications like phage therapy. However, the growing number of computational tools has created a complex landscape, making direct…
Living systems rely on coordinated molecular interactions, especially those related to gene expression and protein activity. The Unfolded Protein Response is a crucial mechanism in eukaryotic cells, activated when unfolded proteins exceed a…
Gene/protein interactions provide critical information for a thorough understanding of cellular processes. Recently, considerable interest and effort has been focused on the construction and analysis of genome-wide gene networks. The large…
Directed protein networks with only a few thousand of nodes are rather complex and do not allow to extract easily the effective influence of one protein to another taking into account all indirect pathways via the global network.…
Identifying interactions between proteins is important to understand underlying biological processes. Extracting a protein-protein interaction (PPI) from the raw text is often very difficult. Previous supervised learning methods have used…
The emergence of cross species interactions at protein level is a part of molecular mechanisms that lead to parasitic diseases. Comprehensive modelling can capture such interactions and could be useful to understand their pathophysiology…
Network theorists have developed methods to characterize the complex interactions in natural phenomena. The structure of the network of interactions between proteins is important in the field of proteomics, and has been subject to intensive…
Protein-protein interactions (PPIs) govern nearly all cellular processes, yet computational methods for identifying binding partners typically produce ranked predictions without mechanistic justification. This creates a fundamental barrier…
The identification of compound-protein interactions (CPI) plays a critical role in drug screening, drug repurposing, and combination therapy studies. The effectiveness of CPI prediction relies heavily on the features extracted from both…
Cancer exhibits diverse and complex phenotypes driven by multifaceted molecular interactions. Recent biomedical research has emphasized the comprehensive study of such diseases by integrating multi-omics datasets (genome, proteome,…
Understanding of how protein interaction networks (PIN) of living organisms have evolved or are organized can be the first stepping stone in unveiling how life works on a fundamental ground. Here we introduce a hybrid network model composed…
Protein-protein interaction networks provide a graph-level view of cellular organization, yet their functional modules are overlapping, noisy, and difficult to interpret from cluster assignments alone. Existing community-detection methods…