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Recent advances in Natural Language Processing (NLP) have ignited interest in developing effective methods for predicting protein-ligand interactions (PLIs) given their relevance to drug discovery and protein engineering efforts and the…
Background: Protein-protein interaction (PPI) network analyses are highly valuable in deciphering and understanding the intricate organisation of cellular functions. Nevertheless, the majority of available protein-protein interaction…
Protein-protein interactions (PPIs) are fundamental to numerous cellular processes, and their characterization is vital for understanding disease mechanisms and guiding drug discovery. While protein language models (PLMs) have demonstrated…
Predicting protein interactions is one of the more interesting challenges of the post-genomic era. Many algorithms address this problem as a binary classification problem: given two proteins represented as two vectors of features, predict…
The worldwide surge of multiresistant microbial strains has propelled the search for alternative treatment options. The study of Protein-Protein Interactions (PPIs) has been a cornerstone in the clarification of complex physiological and…
Specific protein-protein interactions are crucial in the cell, both to ensure the formation and stability of multi-protein complexes, and to enable signal transduction in various pathways. Functional interactions between proteins result in…
Proteins congregate into complexes to perform fundamental cellular functions. Phenotypic outcomes, in health and disease, are often mechanistically driven by the remodeling of protein complexes by protein coding mutations or cellular…
Aligning protein-protein interaction (PPI) networks of different species has drawn a considerable interest recently. This problem is important to investigate evolutionary conserved pathways or protein complexes across species, and to help…
Many protein-protein interaction (PPI) networks take place in the fluid yet structured plasma membrane. Lipid domains, sometimes termed rafts, have been implicated in the functioning of various membrane-bound signaling processes. Here, we…
Advances in sequencing have revealed that each individual carries about 10,000 missense variants. For the vast majority, we do not know what the functional consequences - if any - will be. Further, mechanistic insight, such as structural…
Protein-protein interaction (PPI) extraction from published scientific literature provides additional support for precision medicine efforts. However, many of the current PPI extraction methods need extensive feature engineering and cannot…
Adverse drug interactions are largely preventable causes of medical accidents, which frequently result in physician and emergency room encounters. The detection of drug interactions in a lab, prior to a drug's use in medical practice, is…
High-throughput protein interaction detection methods are strongly affected by false positive and false negative results. Focused experiments are needed to complement the large-scale methods by validating previously detected interactions…
Proteins interact with other proteins within biological pathways, forming connected subgraphs in the protein-protein interactome (PPI). Proteins are often involved in multiple biological pathways which complicates interpretation of…
Accurate systems for extracting Protein-Protein Interactions (PPIs) automatically from biomedical articles can help accelerate biomedical research. Biomedical Informatics researchers are collaborating to provide metaservices and advance the…
Recent advances in AI for science have highlighted the power of contrastive learning in bridging heterogeneous biological data modalities. Building on this paradigm, we propose HIPPO (HIerarchical Protein-Protein interaction prediction…
Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
Deep learning approaches achieved significant progress in predicting protein structures. These methods are often applied to protein-protein interactions (PPIs) yet require Multiple Sequence Alignment (MSA) which is unavailable for various…
Given the vastness of chemical space and the ongoing emergence of previously uncharacterized proteins, zero-shot compound-protein interaction (CPI) prediction better reflects the practical challenges and requirements of real-world drug…
Protein-protein interactions are central mediators in many biological processes. Accurately predicting the effects of mutations on interactions is crucial for guiding the modulation of these interactions, thereby playing a significant role…